Fri Oct 9 15:25:53 BST 2015 ############### You are running ARP/wARP 7.6 ############### Working directory /Users/andrey/Xtal/ArpWarp/Z1 Job ID is set to . X-ray data file /Applications/Xtal70/arp_warp_7.6/examples/Tracing/PSP/psp.mtz Tracing mode WARPNTRACEPHASES Accepted label: fp=FP Accepted label: sigfp=SIGFP Guessed label: phibest=PHIDM Guessed label: fom=FOMDM mtz labels taken: FP SIGFP PHIDM FOMDM Parameter file /Users/andrey/Xtal/ArpWarp/Z1/arp_warp_tracing.par Job launched in /Users/andrey/Xtal/ArpWarp/Z1 ############### You are running ARP/wARP 7.6 ############### ================================================================================== | Please cite at least one of the publications below for | | the ARP/wARP application you are using: | | | | Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular | | model building for x-ray crystallography using ARP/wARP version 7. | | Nat. Protoc. 3, 1171-1179 | | | | Perrakis A, Morris RM, Lamzin VS. (1999) Automated protein model building | | combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 | | | | Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual | | automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. | | 69, 635-641 | | | | Use of Refmac is an essential part of model building with ARP/wARP. | | Please acknowledge the use of Refmac by citing the following publication: | | | | Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, | | Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular | | crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 | ================================================================================== Fri Oct 9 15:26:03 BST 2015 You are running ARP/wARP version 7.6 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /Users/andrey/Xtal/ArpWarp/Z1 ARP/wARP software version: 7.6 The parameter file: /Users/andrey/Xtal/ArpWarp/Z1/arp_warp_tracing.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 630 and 0 Target number of residues in the AU: 630 Target solvent content: 0.4688 Input MTZ file: psp.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP PHIDM FOMDM Space group number: 5 Cell parameters: 107.190 90.610 70.590 90.000 110.570 90.000 Building free atoms model in initial map for 5040 target number of atoms Had to go as low as 0.50 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling, No bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Resolution range: 19.842 2.000 Wilson plot Bfac: 17.64 42570 reflections ( 99.66 % complete ) and 0 restraints for refining 5647 atoms. Observations/parameters ratio is 1.88 ------------------------------------------------------ Starting model: R = 0.3749 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3240 (Rfree = 0.000) for 5647 atoms. Found 122 (193 requested) and removed 96 (96 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.07 2.16 Round 1: 336 peptides, 43 chains. Longest chain 18 peptides. Score 0.581 Round 2: 380 peptides, 28 chains. Longest chain 40 peptides. Score 0.761 Round 3: 390 peptides, 22 chains. Longest chain 44 peptides. Score 0.807 Round 4: 403 peptides, 20 chains. Longest chain 77 peptides. Score 0.830 Round 5: 417 peptides, 18 chains. Longest chain 57 peptides. Score 0.851 Taking the results from Round 5 Chains 18, Residues 399, Estimated correctness of the model 98.2 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 4984 restraints for refining 3789 atoms. 3000 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3815 (Rfree = 0.000) for 3789 atoms. Found 169 (169 requested) and removed 84 (84 requested) atoms. Cycle 2: After refmac, R = 0.3339 (Rfree = 0.000) for 3874 atoms. Found 132 (132 requested) and removed 66 (66 requested) atoms. Cycle 3: After refmac, R = 0.2992 (Rfree = 0.000) for 3939 atoms. Found 134 (134 requested) and removed 67 (67 requested) atoms. Cycle 4: After refmac, R = 0.2746 (Rfree = 0.000) for 4005 atoms. Found 137 (137 requested) and removed 56 (68 requested) atoms. Cycle 5: After refmac, R = 0.2573 (Rfree = 0.000) for 4086 atoms. Found 111 (139 requested) and removed 52 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.84 1.92 Round 1: 435 peptides, 17 chains. Longest chain 66 peptides. Score 0.869 Round 2: 446 peptides, 11 chains. Longest chain 84 peptides. Score 0.899 Round 3: 454 peptides, 10 chains. Longest chain 149 peptides. Score 0.907 Round 4: 452 peptides, 8 chains. Longest chain 182 peptides. Score 0.913 Round 5: 452 peptides, 8 chains. Longest chain 177 peptides. Score 0.913 Taking the results from Round 5 Chains 8, Residues 444, Estimated correctness of the model 99.4 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3775 restraints for refining 3513 atoms. 1350 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3131 (Rfree = 0.000) for 3513 atoms. Found 142 (142 requested) and removed 71 (71 requested) atoms. Cycle 7: After refmac, R = 0.2649 (Rfree = 0.000) for 3584 atoms. Found 122 (122 requested) and removed 61 (61 requested) atoms. Cycle 8: After refmac, R = 0.2366 (Rfree = 0.000) for 3645 atoms. Found 124 (124 requested) and removed 59 (62 requested) atoms. Cycle 9: After refmac, R = 0.2157 (Rfree = 0.000) for 3706 atoms. Found 127 (127 requested) and removed 48 (63 requested) atoms. Cycle 10: After refmac, R = 0.1997 (Rfree = 0.000) for 3784 atoms. Found 129 (129 requested) and removed 38 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.85 1.93 Round 1: 458 peptides, 4 chains. Longest chain 308 peptides. Score 0.929 Round 2: 458 peptides, 5 chains. Longest chain 242 peptides. Score 0.925 Round 3: 461 peptides, 5 chains. Longest chain 245 peptides. Score 0.927 Round 4: 465 peptides, 4 chains. Longest chain 308 peptides. Score 0.932 Round 5: 461 peptides, 5 chains. Longest chain 242 peptides. Score 0.927 Taking the results from Round 4 Chains 4, Residues 461, Estimated correctness of the model 99.6 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3216 restraints for refining 3400 atoms. 570 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2814 (Rfree = 0.000) for 3400 atoms. Found 133 (133 requested) and removed 60 (66 requested) atoms. Cycle 12: After refmac, R = 0.2356 (Rfree = 0.000) for 3472 atoms. Found 118 (118 requested) and removed 37 (59 requested) atoms. Cycle 13: After refmac, R = 0.2085 (Rfree = 0.000) for 3552 atoms. Found 121 (121 requested) and removed 26 (60 requested) atoms. Cycle 14: After refmac, R = 0.1901 (Rfree = 0.000) for 3645 atoms. Found 124 (124 requested) and removed 24 (62 requested) atoms. Cycle 15: After refmac, R = 0.1788 (Rfree = 0.000) for 3741 atoms. Found 128 (128 requested) and removed 26 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.84 1.92 Round 1: 463 peptides, 5 chains. Longest chain 230 peptides. Score 0.928 Round 2: 464 peptides, 5 chains. Longest chain 180 peptides. Score 0.928 Round 3: 462 peptides, 6 chains. Longest chain 137 peptides. Score 0.924 Round 4: 462 peptides, 6 chains. Longest chain 180 peptides. Score 0.924 Round 5: 462 peptides, 5 chains. Longest chain 183 peptides. Score 0.927 Taking the results from Round 2 Chains 5, Residues 459, Estimated correctness of the model 99.6 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3147 restraints for refining 3351 atoms. 474 conditional restraints added. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2698 (Rfree = 0.000) for 3351 atoms. Found 131 (131 requested) and removed 39 (65 requested) atoms. Cycle 17: After refmac, R = 0.2266 (Rfree = 0.000) for 3443 atoms. Found 117 (117 requested) and removed 15 (58 requested) atoms. Cycle 18: After refmac, R = 0.2010 (Rfree = 0.000) for 3545 atoms. Found 121 (121 requested) and removed 12 (60 requested) atoms. Cycle 19: After refmac, R = 0.1851 (Rfree = 0.000) for 3652 atoms. Found 125 (125 requested) and removed 11 (62 requested) atoms. Cycle 20: After refmac, R = 0.1738 (Rfree = 0.000) for 3763 atoms. Found 129 (129 requested) and removed 22 (64 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.85 1.93 Round 1: 466 peptides, 3 chains. Longest chain 308 peptides. Score 0.935 Round 2: 467 peptides, 3 chains. Longest chain 308 peptides. Score 0.935 Round 3: 466 peptides, 4 chains. Longest chain 230 peptides. Score 0.932 Round 4: 464 peptides, 6 chains. Longest chain 137 peptides. Score 0.925 Round 5: 467 peptides, 5 chains. Longest chain 171 peptides. Score 0.929 Taking the results from Round 2 Chains 3, Residues 464, Estimated correctness of the model 99.7 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3139 restraints for refining 3400 atoms. 425 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2678 (Rfree = 0.000) for 3400 atoms. Found 132 (132 requested) and removed 47 (66 requested) atoms. Cycle 22: After refmac, R = 0.2240 (Rfree = 0.000) for 3484 atoms. Found 119 (119 requested) and removed 13 (59 requested) atoms. Cycle 23: After refmac, R = 0.1961 (Rfree = 0.000) for 3589 atoms. Found 122 (122 requested) and removed 7 (61 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 3701 atoms. Found 126 (126 requested) and removed 9 (63 requested) atoms. Cycle 25: After refmac, R = 0.1691 (Rfree = 0.000) for 3814 atoms. Found 115 (130 requested) and removed 20 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.84 1.92 Round 1: 467 peptides, 5 chains. Longest chain 164 peptides. Score 0.929 Round 2: 467 peptides, 4 chains. Longest chain 246 peptides. Score 0.932 Round 3: 467 peptides, 5 chains. Longest chain 165 peptides. Score 0.929 Round 4: 465 peptides, 7 chains. Longest chain 95 peptides. Score 0.922 Round 5: 462 peptides, 5 chains. Longest chain 228 peptides. Score 0.927 Taking the results from Round 2 Chains 4, Residues 463, Estimated correctness of the model 99.6 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3149 restraints for refining 3394 atoms. 444 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2666 (Rfree = 0.000) for 3394 atoms. Found 133 (133 requested) and removed 49 (66 requested) atoms. Cycle 27: After refmac, R = 0.2233 (Rfree = 0.000) for 3478 atoms. Found 119 (119 requested) and removed 14 (59 requested) atoms. Cycle 28: After refmac, R = 0.1943 (Rfree = 0.000) for 3582 atoms. Found 122 (122 requested) and removed 10 (61 requested) atoms. Cycle 29: After refmac, R = 0.1783 (Rfree = 0.000) for 3691 atoms. Found 126 (126 requested) and removed 9 (63 requested) atoms. Cycle 30: After refmac, R = 0.1676 (Rfree = 0.000) for 3803 atoms. Found 128 (130 requested) and removed 19 (65 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.84 1.92 Round 1: 465 peptides, 5 chains. Longest chain 230 peptides. Score 0.928 Round 2: 466 peptides, 6 chains. Longest chain 115 peptides. Score 0.926 Round 3: 470 peptides, 3 chains. Longest chain 181 peptides. Score 0.937 Round 4: 471 peptides, 2 chains. Longest chain 308 peptides. Score 0.940 Round 5: 471 peptides, 3 chains. Longest chain 245 peptides. Score 0.937 Taking the results from Round 4 Chains 2, Residues 469, Estimated correctness of the model 99.7 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3139 restraints for refining 3416 atoms. 412 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 3416 atoms. Found 134 (134 requested) and removed 53 (67 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 3497 atoms. Found 119 (119 requested) and removed 17 (59 requested) atoms. Cycle 33: After refmac, R = 0.1969 (Rfree = 0.000) for 3598 atoms. Found 123 (123 requested) and removed 11 (61 requested) atoms. Cycle 34: After refmac, R = 0.1814 (Rfree = 0.000) for 3707 atoms. Found 127 (127 requested) and removed 10 (63 requested) atoms. Cycle 35: After refmac, R = 0.1700 (Rfree = 0.000) for 3819 atoms. Found 116 (130 requested) and removed 27 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.85 1.93 Round 1: 469 peptides, 3 chains. Longest chain 308 peptides. Score 0.936 Round 2: 469 peptides, 3 chains. Longest chain 308 peptides. Score 0.936 Round 3: 468 peptides, 4 chains. Longest chain 258 peptides. Score 0.933 Round 4: 471 peptides, 5 chains. Longest chain 309 peptides. Score 0.931 Round 5: 471 peptides, 4 chains. Longest chain 255 peptides. Score 0.934 Taking the results from Round 2 Chains 3, Residues 466, Estimated correctness of the model 99.7 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3085 restraints for refining 3388 atoms. 369 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2661 (Rfree = 0.000) for 3388 atoms. Found 133 (133 requested) and removed 52 (66 requested) atoms. Cycle 37: After refmac, R = 0.2230 (Rfree = 0.000) for 3468 atoms. Found 118 (118 requested) and removed 18 (59 requested) atoms. Cycle 38: After refmac, R = 0.1982 (Rfree = 0.000) for 3566 atoms. Found 122 (122 requested) and removed 7 (61 requested) atoms. Cycle 39: After refmac, R = 0.1788 (Rfree = 0.000) for 3680 atoms. Found 126 (126 requested) and removed 7 (63 requested) atoms. Cycle 40: After refmac, R = 0.1681 (Rfree = 0.000) for 3796 atoms. Found 103 (130 requested) and removed 13 (65 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.85 1.93 Round 1: 468 peptides, 3 chains. Longest chain 308 peptides. Score 0.936 Round 2: 468 peptides, 4 chains. Longest chain 230 peptides. Score 0.933 Round 3: 473 peptides, 2 chains. Longest chain 399 peptides. Score 0.941 Round 4: 473 peptides, 2 chains. Longest chain 399 peptides. Score 0.941 Round 5: 471 peptides, 3 chains. Longest chain 311 peptides. Score 0.937 Taking the results from Round 4 Chains 2, Residues 471, Estimated correctness of the model 99.7 % ------------------------------------------------------ 42570 reflections ( 99.66 % complete ) and 3094 restraints for refining 3385 atoms. 368 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2714 (Rfree = 0.000) for 3385 atoms. Found 133 (133 requested) and removed 46 (66 requested) atoms. Cycle 42: After refmac, R = 0.2254 (Rfree = 0.000) for 3472 atoms. Found 118 (118 requested) and removed 13 (59 requested) atoms. Cycle 43: After refmac, R = 0.1970 (Rfree = 0.000) for 3575 atoms. Found 122 (122 requested) and removed 7 (61 requested) atoms. Cycle 44: After refmac, R = 0.1808 (Rfree = 0.000) for 3687 atoms. Found 126 (126 requested) and removed 12 (63 requested) atoms. Cycle 45: After refmac, R = 0.1680 (Rfree = 0.000) for 3797 atoms. Found 121 (130 requested) and removed 19 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.84 1.92 Round 1: 471 peptides, 3 chains. Longest chain 309 peptides. Score 0.937 Round 2: 471 peptides, 4 chains. Longest chain 255 peptides. Score 0.934 Round 3: 470 peptides, 4 chains. Longest chain 309 peptides. Score 0.934 Round 4: 470 peptides, 4 chains. Longest chain 175 peptides. Score 0.934 Round 5: 467 peptides, 5 chains. Longest chain 222 peptides. Score 0.929 Taking the results from Round 1 Chains 3, Residues 468, Estimated correctness of the model 99.7 % ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 42570 reflections ( 99.66 % complete ) and 3066 restraints for refining 3375 atoms. 338 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2653 (Rfree = 0.000) for 3375 atoms. Found 0 (133 requested) and removed 9 (66 requested) atoms. Cycle 47: After refmac, R = 0.2539 (Rfree = 0.000) for 3366 atoms. Found 0 (115 requested) and removed 5 (57 requested) atoms. Cycle 48: After refmac, R = 0.2483 (Rfree = 0.000) for 3361 atoms. Found 0 (115 requested) and removed 1 (57 requested) atoms. Cycle 49: After refmac, R = 0.2454 (Rfree = 0.000) for 3360 atoms. Found 0 (115 requested) and removed 1 (57 requested) atoms. Writing map files covering molecule ... Normal termination of warpNtrace Fri Oct 9 16:11:38 BST 2015 Job finished.