The following parameters have been modified: input { datablock = datablock.json reflections = strong.pickle } Found max_cell: 199.0 Angstrom Setting d_min: 3.89 FFT gridding: (256,256,256) Number of centroids used: 13298 model 1 (13245 reflections): Crystal: Unit cell: (57.927, 58.377, 150.126, 89.734, 89.796, 89.680) Space group: P 1 U matrix: {{ 0.3455, -0.2607, -0.9015}, { 0.8911, 0.3923, 0.2281}, { 0.2942, -0.8821, 0.3679}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0001, 0.0171, 0.0000}, {-0.0001, -0.0001, 0.0067}} A = UB: {{ 0.0060, -0.0044, -0.0060}, { 0.0153, 0.0067, 0.0015}, { 0.0051, -0.0151, 0.0025}} 43 unindexed reflections ################################################################################ Starting refinement (macro-cycle 1) ################################################################################ Summary statistics for 12585 observations matched to predictions: ------------------------------------------------------------------------ | | Min | Q1 | Med | Q3 | Max | ------------------------------------------------------------------------ | Xc - Xo (mm) | -0.6282 | -0.3151 | -0.2315 | -0.1485 | 0.5033 | | Yc - Yo (mm) | -0.8444 | -0.2148 | -0.1216 | -0.03768 | 0.3894 | | Phic - Phio (deg) | -0.8988 | -0.2314 | -0.06123 | 0.04194 | 1.035 | | X weights | 253.5 | 401.7 | 404.2 | 405.1 | 405.6 | | Y weights | 260.5 | 402.6 | 404.5 | 405.3 | 405.6 | | Phi weights | 416.1 | 527.9 | 531 | 532.2 | 533.3 | ------------------------------------------------------------------------ 2448 reflections have been flagged as outliers Summary statistics for 10137 observations matched to predictions: ------------------------------------------------------------------------ | | Min | Q1 | Med | Q3 | Max | ------------------------------------------------------------------------ | Xc - Xo (mm) | -0.5793 | -0.307 | -0.2343 | -0.1609 | 0.1994 | | Yc - Yo (mm) | -0.477 | -0.2013 | -0.1174 | -0.02053 | 0.3894 | | Phic - Phio (deg) | -0.404 | -0.1352 | -0.01158 | 0.05198 | 0.3607 | | X weights | 272.3 | 401.8 | 404.2 | 405.1 | 405.6 | | Y weights | 260.5 | 402.6 | 404.5 | 405.3 | 405.6 | | Phi weights | 416.1 | 527.7 | 530.8 | 532.1 | 533.3 | ------------------------------------------------------------------------ Refinement steps: ------------------------------------------------ | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------ | 0 | 8099 | 0.26351 | 0.17489 | 0.12937 | | 1 | 8099 | 0.04359 | 0.048009 | 0.066931 | | 2 | 8099 | 0.038391 | 0.043164 | 0.04162 | | 3 | 8099 | 0.03623 | 0.041487 | 0.027362 | | 4 | 8099 | 0.034786 | 0.038974 | 0.019906 | | 5 | 8099 | 0.033455 | 0.036678 | 0.015428 | | 6 | 8099 | 0.031924 | 0.034589 | 0.014346 | | 7 | 8099 | 0.031019 | 0.03339 | 0.014189 | ------------------------------------------------ RMSD target achieved RMSDs by experiment: --------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | --------------------------------------------- | 0 | 8099 | 0.18035 | 0.19413 | 0.094595 | --------------------------------------------- Using d_min_step 0.7 Increasing resolution to 3.2 Angstrom model 1 (23310 reflections): Crystal: Unit cell: (57.811, 57.789, 150.043, 89.996, 89.973, 89.988) Space group: P 1 U matrix: {{ 0.3453, -0.2591, -0.9020}, { 0.8915, 0.3909, 0.2290}, { 0.2933, -0.8832, 0.3660}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0000, 0.0173, 0.0000}, {-0.0000, -0.0000, 0.0067}} A = UB: {{ 0.0060, -0.0045, -0.0060}, { 0.0154, 0.0068, 0.0015}, { 0.0051, -0.0153, 0.0024}} 121 unindexed reflections ################################################################################ Starting refinement (macro-cycle 2) ################################################################################ Summary statistics for 22493 observations matched to predictions: -------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | -------------------------------------------------------------------------- | Xc - Xo (mm) | -0.2816 | -0.02505 | -0.005411 | 0.02864 | 0.2515 | | Yc - Yo (mm) | -0.7145 | -0.02142 | -0.0004552 | 0.01996 | 0.2835 | | Phic - Phio (deg) | -1.051 | -0.01046 | -0.0006884 | 0.0096 | 0.905 | | X weights | 243.1 | 400.9 | 403.8 | 404.9 | 405.6 | | Y weights | 239.1 | 401.3 | 404 | 405 | 405.6 | | Phi weights | 401.5 | 527.6 | 530.8 | 532.2 | 533.3 | -------------------------------------------------------------------------- 1653 reflections have been flagged as outliers Summary statistics for 20840 observations matched to predictions: ----------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | ----------------------------------------------------------------------------- | Xc - Xo (mm) | -0.1169 | -0.0223 | -0.003617 | 0.03081 | 0.1198 | | Yc - Yo (mm) | -0.09175 | -0.02192 | -0.001916 | 0.01659 | 0.08541 | | Phic - Phio (deg) | -0.04497 | -0.01023 | -0.0006471 | 0.009448 | 0.04195 | | X weights | 243.1 | 401.1 | 403.8 | 404.9 | 405.6 | | Y weights | 260.5 | 401.4 | 404 | 405 | 405.6 | | Phi weights | 419 | 527.6 | 530.8 | 532.2 | 533.3 | ----------------------------------------------------------------------------- Refinement steps: ------------------------------------------------ | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------ | 0 | 8099 | 0.037562 | 0.028801 | 0.014065 | | 1 | 8099 | 0.03615 | 0.028519 | 0.014034 | | 2 | 8099 | 0.036101 | 0.02844 | 0.013976 | | 3 | 8099 | 0.03601 | 0.02835 | 0.013919 | | 4 | 8099 | 0.035814 | 0.028251 | 0.013892 | | 5 | 8099 | 0.035406 | 0.02811 | 0.013878 | | 6 | 8099 | 0.034861 | 0.028049 | 0.013852 | | 7 | 8099 | 0.034523 | 0.028151 | 0.013828 | | 8 | 8099 | 0.034439 | 0.028218 | 0.01382 | | 9 | 8099 | 0.034431 | 0.028227 | 0.013819 | | 10 | 8099 | 0.034431 | 0.028228 | 0.013818 | ------------------------------------------------ RMSD no longer decreasing RMSDs by experiment: --------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | --------------------------------------------- | 0 | 8099 | 0.20018 | 0.16411 | 0.092123 | --------------------------------------------- Increasing resolution to 2.6 Angstrom model 1 (43346 reflections): Crystal: Unit cell: (57.803, 57.774, 150.032, 90.013, 89.986, 89.985) Space group: P 1 U matrix: {{ 0.3455, -0.2590, -0.9020}, { 0.8914, 0.3909, 0.2292}, { 0.2932, -0.8832, 0.3659}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0000, 0.0173, 0.0000}, {-0.0000, 0.0000, 0.0067}} A = UB: {{ 0.0060, -0.0045, -0.0060}, { 0.0154, 0.0068, 0.0015}, { 0.0051, -0.0153, 0.0024}} 137 unindexed reflections ################################################################################ Starting refinement (macro-cycle 3) ################################################################################ Summary statistics for 42351 observations matched to predictions: -------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | -------------------------------------------------------------------------- | Xc - Xo (mm) | -0.5012 | -0.02516 | 0.006709 | 0.0326 | 0.2609 | | Yc - Yo (mm) | -0.704 | -0.01313 | 0.006151 | 0.02701 | 0.2916 | | Phic - Phio (deg) | -1.052 | -0.01075 | -0.0004882 | 0.01031 | 0.9074 | | X weights | 202.8 | 396.9 | 402.3 | 404.5 | 405.6 | | Y weights | 210.9 | 396.1 | 402.2 | 404.5 | 405.6 | | Phi weights | 386.4 | 524.9 | 530 | 532.1 | 533.3 | -------------------------------------------------------------------------- 2604 reflections have been flagged as outliers Summary statistics for 39747 observations matched to predictions: ----------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | ----------------------------------------------------------------------------- | Xc - Xo (mm) | -0.1008 | -0.02292 | 0.007548 | 0.03216 | 0.1216 | | Yc - Yo (mm) | -0.08829 | -0.01313 | 0.005374 | 0.02507 | 0.09138 | | Phic - Phio (deg) | -0.05139 | -0.01036 | -0.0004898 | 0.009936 | 0.05098 | | X weights | 231.1 | 397.5 | 402.5 | 404.5 | 405.6 | | Y weights | 231.2 | 396.7 | 402.3 | 404.5 | 405.6 | | Phi weights | 399.5 | 525 | 530 | 532.1 | 533.3 | ----------------------------------------------------------------------------- Refinement steps: ------------------------------------------------ | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------ | 0 | 8099 | 0.041131 | 0.028769 | 0.014744 | | 1 | 8099 | 0.038326 | 0.028061 | 0.015152 | | 2 | 8099 | 0.038311 | 0.028057 | 0.015084 | | 3 | 8099 | 0.038287 | 0.028028 | 0.01499 | | 4 | 8099 | 0.038244 | 0.02794 | 0.014908 | | 5 | 8099 | 0.038169 | 0.027766 | 0.014871 | | 6 | 8099 | 0.038061 | 0.027586 | 0.014865 | | 7 | 8099 | 0.037957 | 0.027548 | 0.014872 | | 8 | 8099 | 0.037909 | 0.027583 | 0.014881 | | 9 | 8099 | 0.0379 | 0.027593 | 0.014883 | | 10 | 8099 | 0.0379 | 0.027593 | 0.014883 | ------------------------------------------------ RMSD no longer decreasing RMSDs by experiment: --------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | --------------------------------------------- | 0 | 8099 | 0.22035 | 0.16043 | 0.099218 | --------------------------------------------- Increasing resolution to 1.9 Angstrom model 1 (89300 reflections): Crystal: Unit cell: (57.816, 57.781, 150.030, 90.020, 89.997, 89.987) Space group: P 1 U matrix: {{ 0.3455, -0.2588, -0.9020}, { 0.8914, 0.3909, 0.2293}, { 0.2932, -0.8833, 0.3658}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0000, 0.0173, 0.0000}, {-0.0000, 0.0000, 0.0067}} A = UB: {{ 0.0060, -0.0045, -0.0060}, { 0.0154, 0.0068, 0.0015}, { 0.0051, -0.0153, 0.0024}} 300 unindexed reflections ################################################################################ Starting refinement (macro-cycle 4) ################################################################################ Summary statistics for 88041 observations matched to predictions: -------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | -------------------------------------------------------------------------- | Xc - Xo (mm) | -0.4767 | -0.02958 | 0.001571 | 0.03312 | 0.6737 | | Yc - Yo (mm) | -1.42 | -0.01996 | 0.003176 | 0.02597 | 1.432 | | Phic - Phio (deg) | -1.434 | -0.01299 | -0.0004573 | 0.01265 | 0.9043 | | X weights | 202.8 | 384.6 | 397.4 | 403.3 | 405.6 | | Y weights | 171 | 378.6 | 395 | 402.6 | 405.6 | | Phi weights | 318.9 | 520.3 | 529.4 | 533.3 | 533.3 | -------------------------------------------------------------------------- 8384 reflections have been flagged as outliers Summary statistics for 79657 observations matched to predictions: --------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | --------------------------------------------------------------------------- | Xc - Xo (mm) | -0.1483 | -0.028 | 0.002817 | 0.03259 | 0.1453 | | Yc - Yo (mm) | -0.09244 | -0.01713 | 0.003795 | 0.02505 | 0.09839 | | Phic - Phio (deg) | -0.05483 | -0.01184 | -0.000235 | 0.01191 | 0.0556 | | X weights | 205 | 387.5 | 398.3 | 403.5 | 405.6 | | Y weights | 171 | 382.7 | 396.4 | 402.9 | 405.6 | | Phi weights | 318.9 | 520.4 | 529.1 | 533 | 533.3 | --------------------------------------------------------------------------- Refinement steps: ------------------------------------------------ | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------ | 0 | 8099 | 0.042412 | 0.033194 | 0.017463 | | 1 | 8099 | 0.041445 | 0.032572 | 0.017543 | | 2 | 8099 | 0.041436 | 0.032546 | 0.017495 | | 3 | 8099 | 0.041429 | 0.032461 | 0.017445 | | 4 | 8099 | 0.041425 | 0.032271 | 0.017404 | | 5 | 8099 | 0.041458 | 0.031963 | 0.017375 | | 6 | 8099 | 0.041544 | 0.031644 | 0.017351 | | 7 | 8099 | 0.041621 | 0.031457 | 0.017343 | | 8 | 8099 | 0.041651 | 0.031405 | 0.017343 | | 9 | 8099 | 0.041656 | 0.031398 | 0.017343 | | 10 | 8099 | 0.041656 | 0.031398 | 0.017343 | ------------------------------------------------ RMSD no longer decreasing RMSDs by experiment: --------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | --------------------------------------------- | 0 | 8099 | 0.24219 | 0.18254 | 0.11562 | --------------------------------------------- Increasing resolution to 1.3 Angstrom model 1 (114690 reflections): Crystal: Unit cell: (57.815, 57.783, 150.035, 90.016, 89.991, 89.988) Space group: P 1 U matrix: {{ 0.3455, -0.2589, -0.9020}, { 0.8914, 0.3909, 0.2292}, { 0.2933, -0.8833, 0.3658}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0000, 0.0173, 0.0000}, {-0.0000, 0.0000, 0.0067}} A = UB: {{ 0.0060, -0.0045, -0.0060}, { 0.0154, 0.0068, 0.0015}, { 0.0051, -0.0153, 0.0024}} 342 unindexed reflections ################################################################################ Starting refinement (macro-cycle 5) ################################################################################ Summary statistics for 113247 observations matched to predictions: -------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | -------------------------------------------------------------------------- | Xc - Xo (mm) | -0.5332 | -0.03414 | -0.004714 | 0.02995 | 0.6695 | | Yc - Yo (mm) | -1.422 | -0.03176 | -0.003558 | 0.01999 | 1.273 | | Phic - Phio (deg) | -1.427 | -0.01451 | -0.0005735 | 0.01382 | 0.9041 | | X weights | 135.2 | 371.6 | 393.4 | 402.6 | 405.6 | | Y weights | 153.1 | 361.8 | 389 | 401.2 | 405.6 | | Phi weights | 318.9 | 519.5 | 530.4 | 533.3 | 533.3 | -------------------------------------------------------------------------- 15804 reflections have been flagged as outliers Summary statistics for 97443 observations matched to predictions: ---------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | ---------------------------------------------------------------------------- | Xc - Xo (mm) | -0.1543 | -0.03126 | -0.003093 | 0.02881 | 0.1455 | | Yc - Yo (mm) | -0.1028 | -0.02321 | -0.0006546 | 0.0205 | 0.1025 | | Phic - Phio (deg) | -0.06064 | -0.01269 | -0.0003442 | 0.01256 | 0.06094 | | X weights | 135.2 | 379.3 | 395.7 | 403 | 405.6 | | Y weights | 162.2 | 372.1 | 392.6 | 402 | 405.6 | | Phi weights | 318.9 | 519.4 | 529.7 | 533.3 | 533.3 | ---------------------------------------------------------------------------- Refinement steps: ------------------------------------------------ | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------ | 0 | 8099 | 0.043616 | 0.033904 | 0.019225 | | 1 | 8099 | 0.043394 | 0.033843 | 0.019184 | | 2 | 8099 | 0.043371 | 0.033778 | 0.019175 | | 3 | 8099 | 0.043321 | 0.033677 | 0.019169 | | 4 | 8099 | 0.043235 | 0.033557 | 0.019171 | | 5 | 8099 | 0.043138 | 0.033443 | 0.019179 | | 6 | 8099 | 0.043081 | 0.033365 | 0.019197 | | 7 | 8099 | 0.043068 | 0.033318 | 0.019215 | | 8 | 8099 | 0.043069 | 0.033302 | 0.019224 | | 9 | 8099 | 0.04307 | 0.0333 | 0.019225 | ------------------------------------------------ RMSD no longer decreasing RMSDs by experiment: -------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | -------------------------------------------- | 0 | 8099 | 0.25041 | 0.1936 | 0.12817 | -------------------------------------------- Final refined crystal models: model 1 (114690 reflections): Crystal: Unit cell: (57.814, 57.784, 150.035, 90.012, 89.989, 89.988) Space group: P 1 U matrix: {{ 0.3454, -0.2589, -0.9020}, { 0.8914, 0.3909, 0.2292}, { 0.2933, -0.8833, 0.3658}} B matrix: {{ 0.0173, 0.0000, 0.0000}, {-0.0000, 0.0173, 0.0000}, {-0.0000, 0.0000, 0.0067}} A = UB: {{ 0.0060, -0.0045, -0.0060}, { 0.0154, 0.0068, 0.0015}, { 0.0051, -0.0153, 0.0024}} Saving refined experiments to experiments.json Saving refined reflections to indexed.pickle