# Servalcat ver. 0.4.77 (Python 3.9.18) # Library vers. gemmi 0.6.6, scipy 1.7.3, numpy 1.19.5, pandas 1.3.5 # Started on 2024-08-12 12:49:40.261774 # Host: anaconda.lbl.gov User: afonine # Command-line: # servalcat refine_spa --map ../../../../cryoem/start/7oko_12963.map --model ../../../../cryoem/start/7oko_12963.pdb ERROR: --resolution is needed. # Servalcat ver. 0.4.77 (Python 3.9.18) # Library vers. gemmi 0.6.6, scipy 1.7.3, numpy 1.19.5, pandas 1.3.5 # Started on 2024-08-12 12:49:49.455361 # Host: anaconda.lbl.gov User: afonine # Command-line: # servalcat refine_spa --map ../../../../cryoem/start/7oko_12963.map --model ../../../../cryoem/start/7oko_12963.pdb --resolution 3 Refmac version: 5.8.0430 will use gemmi to prepare restraints Input model: ../../../../cryoem/start/7oko_12963.pdb Reading PDB file: ../../../../cryoem/start/7oko_12963.pdb Unit cell: 125.4000 66.0000 96.8000 90.000 90.000 90.000 Space group: P 1 Reading monomers from /net/anaconda/raid1/afonine/work/CCP4/ccp4-9/lib/data/monomers/ Monomer library loaded: 19 monomers, 109 links, 127 modifications loaded monomers: ALA ARG ASN ASP GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL Checking if unknown atoms exist.. Creating restraints.. Warning: definition not found for 0/ALA 69/H1 Warning: definition not found for 0/THR 157/H1 Warning: definition not found for 1/VAL 158/H1 Warning: definition not found for 2/PRO 177/H3 Warning: definition not found for 3/ALA 24/H1 Chain info: chain 0 PeptideL: 69..204 (60 residues) gap between 80(ARG) and 157(THR) chain 1 PeptideL: 158..203 (46 residues) chain 2 PeptideL: 177..186 (10 residues) chain 3 PeptideL: 24..239 (216 residues) Reading CCP4/MRC map file ../../../../cryoem/start/7oko_12963.map Cell Grid: 114 60 88 Map mode: 2 Start: 0 0 0 Shape: 88 60 114 Cell: 125.4 66.0 96.8 90.0 90.0 90.0 Axis order: Z Y X Space group: 1 Spacing: 1.100000 1.100000 1.100000 Voxel size: 1.100000 1.100000 1.100000 Origin: 0.000000e+00 0.000000e+00 0.000000e+00 Label: boxed Creating mask.. Saving input model with unit cell information Writing mmCIF file: starting_model.mmcif Writing PDB file: starting_model.pdb Applying mask.. Shifting maps and/or model.. Original grid start: 0 0 0 grid end: 113 59 87 Limits: (3, 109) (4, 56) (4, 83) Padding: 6 6 6 Non-centered trimming will be performed. Slices: [slice(0, 114, None), slice(0, 60, None), slice(0, 88, None)] Shift for model: -0.0 -0.0 -0.0 New Cell: 125.4000 66.0000 96.8000 90.000 90.000 90.000 New grid: 114 60 88 Vol_mask/Vol_map= 8.31e-02 Saving model in trimmed map.. Writing mmCIF file: shifted.mmcif Writing PDB file: shifted.pdb Trimming maps.. Checking links defined in the model no links defined in the model Finding new links (will be added if marked by *) no links found Creating restraints.. Chain info: chain 0 PeptideL: 69..204 (60 residues) gap between 80(ARG) and 157(THR) chain 1 PeptideL: 158..203 (46 residues) chain 2 PeptideL: 177..186 (10 residues) chain 3 PeptideL: 24..239 (216 residues) crd file written: shifted.crd Bin 1 only has 2 data. Merging with next bin. Bin 42 only has 1337 data. Merging with previous bin. Saving masked maps as mtz file.. applying phase shift for Fout with translation Writing MTZ file: masked_fs_obs.mtz Estimating weight auto scale using resolution and volume ratio Will use weight auto 1.96 Running REFMAC5.. refmac5 hklin masked_fs_obs.mtz hklout shifted_refined.mtz xyzin shifted.crd xyzout shifted_refined.pdb <<__eof__ > shifted_refined.log labin FP=Fout PHIB=Pout make hydr all make hout no solvent no scale lssc isot source em mb ncycle 10 reso 3.0 weight auto 1.96e+00 ncsr local pdbo keep auth make cr prepared __eof__ Starting Refmac 5.8.0430 (PID: 140579) Warning ==>The number of free reflections with flag -999 is zero Warning ==> Switching off use of free R cycle= 0 FSCaverage= 0.5087 (initial) cycle= 1 FSCaverage= 0.5532 cycle= 2 FSCaverage= 0.5664 cycle= 3 FSCaverage= 0.5820 cycle= 4 FSCaverage= 0.5875 cycle= 5 FSCaverage= 0.5922 cycle= 6 FSCaverage= 0.5953 cycle= 7 FSCaverage= 0.5982 cycle= 8 FSCaverage= 0.6009 cycle= 9 FSCaverage= 0.6036 cycle= 10 FSCaverage= 0.6062 (final) Initial Final Rms BondLength 0.0095 0.0080 Rms BondAngle 1.3177 1.5873 REFMAC5 finished with exit code= 0 Reading mmCIF file: shifted_refined.mmcif Unit cell: 125.4000 66.0000 96.8000 90.000 90.000 90.000 Space group: P 1 = ADP analysis = (zero-occupancy atoms are ignored) min Q1 med Q3 max Chain 0 26.2 67.5 95.9 124.3 339.8 Chain 1 25.7 52.7 74.6 115.3 317.8 Chain 2 62.2 78.9 99.7 118.8 228.4 Chain 3 25.6 60.5 78.4 110.4 387.1 All 25.6 60.6 81.4 115.5 387.1 Writing mmCIF file: refined.mmcif using mmCIF metadata from: shifted_refined.mmcif Writing PDB file: refined.pdb Calculating map-model FSC.. --fsc_resolution is not specified. Using Nyquist resolution: 2.20 Creating restraints.. Chain info: chain 0 PeptideL: 69..204 (60 residues) gap between 80(ARG) and 157(THR) chain 1 PeptideL: 158..203 (46 residues) chain 2 PeptideL: 177..186 (10 residues) chain 3 PeptideL: 24..239 (216 residues) Generating hydrogens at electron positions Setting blur= 13.01 in density calculation (unblurred later) Calculating proton-shifted Fc using Mott-Bethe formula done. Fc calculation time: 0.6 s Bin 1 only has 2 data. Merging with next bin. Bin 1 only has 2 data. Merging with next bin. Bin 42 only has 1336 data. Merging with previous bin. d_min d_max ncoeffs power_FP power_FC fsc_FC_full Rcmplx_FC_full cc_FC_full mcos_FC_full 2 52.624999 125.400000 12 3.356557e+07 1.082491e+07 0.979678 0.181121 0.894736 0.998238 3 37.266656 50.007400 24 1.007000e+07 2.159683e+06 0.998103 0.060968 0.995534 0.997842 4 27.957797 35.313437 47 4.453399e+06 8.941439e+05 0.993878 0.113504 0.987084 0.982602 5 22.836716 27.265502 50 1.449684e+06 2.924851e+05 0.982632 0.186637 0.961648 0.920194 6 19.360000 22.785617 99 7.887492e+05 1.426816e+05 0.971903 0.246467 0.944298 0.940249 7 16.800415 19.282899 121 5.698817e+05 8.675398e+04 0.969734 0.248018 0.927554 0.950886 8 14.912432 16.698482 165 5.558579e+05 8.239897e+04 0.974831 0.227561 0.947435 0.927776 9 13.229944 14.738153 200 3.763048e+05 5.586717e+04 0.965204 0.262079 0.926758 0.929169 10 11.977605 13.200000 267 2.951936e+05 4.257186e+04 0.964834 0.263696 0.913027 0.930746 11 10.906201 11.938916 296 2.181980e+05 2.939666e+04 0.958259 0.288281 0.903856 0.921958 12 10.040295 10.897965 392 1.569067e+05 1.949978e+04 0.946458 0.329347 0.873236 0.910813 13 9.289350 10.027346 429 1.142469e+05 1.359073e+04 0.931495 0.364475 0.856609 0.863159 14 8.659725 9.288628 498 9.171673e+04 1.103610e+04 0.923710 0.385145 0.836344 0.865677 15 8.092785 8.647428 574 7.849618e+04 9.439744e+03 0.930363 0.369382 0.856627 0.856711 16 7.601840 8.083228 664 6.489118e+04 7.845435e+03 0.923656 0.389161 0.842708 0.846342 17 7.172476 7.596765 711 5.409837e+04 6.582378e+03 0.909455 0.409448 0.803269 0.826393 18 6.779852 7.161854 856 4.915773e+04 5.856371e+03 0.909255 0.415689 0.804614 0.832885 19 6.431845 6.777760 909 4.375430e+04 4.983873e+03 0.899112 0.438572 0.787021 0.821941 20 6.117600 6.429543 1005 4.696055e+04 4.693127e+03 0.902871 0.430548 0.786405 0.815531 21 5.832839 6.116409 1149 5.237879e+04 4.755554e+03 0.907205 0.427295 0.815507 0.815645 22 5.573469 5.832209 1226 5.992450e+04 5.033556e+03 0.919585 0.396648 0.822119 0.866335 23 5.337306 5.573277 1357 6.039548e+04 4.648143e+03 0.916035 0.407826 0.821934 0.851986 24 5.119167 5.334429 1443 7.151566e+04 4.826778e+03 0.930876 0.373210 0.852848 0.860726 25 4.917860 5.118365 1607 7.651780e+04 4.639274e+03 0.925622 0.385837 0.843025 0.861238 26 4.732319 4.917013 1752 7.603017e+04 4.070510e+03 0.921776 0.398652 0.847872 0.836071 27 4.560491 4.731836 1857 7.153272e+04 3.533699e+03 0.913673 0.421408 0.834342 0.834053 28 4.400855 4.559783 1917 6.629328e+04 2.931484e+03 0.901393 0.445236 0.805845 0.815720 29 4.250957 4.400000 2259 5.350804e+04 2.205612e+03 0.876310 0.498418 0.783434 0.774810 30 4.112386 4.250796 2263 4.038931e+04 1.618575e+03 0.840137 0.555574 0.717241 0.733734 31 3.981100 4.111283 2492 2.768614e+04 1.224212e+03 0.802124 0.612795 0.667463 0.677620 32 3.858990 3.980128 2547 1.787262e+04 8.992892e+02 0.752368 0.667989 0.575093 0.625197 33 3.743325 3.858030 2807 1.162354e+04 6.892119e+02 0.681212 0.744010 0.496977 0.542047 34 3.634893 3.743165 2933 8.456579e+03 5.541987e+02 0.618503 0.797301 0.390322 0.486469 35 3.532430 3.634508 3170 6.286788e+03 4.522013e+02 0.558739 0.842508 0.326311 0.435802 36 3.435718 3.532328 3255 4.631393e+03 3.689320e+02 0.487192 0.882877 0.270899 0.370653 37 3.344335 3.435565 3539 3.160493e+03 3.073017e+02 0.421972 0.915883 0.191486 0.327365 38 3.257328 3.343896 3695 2.180141e+03 2.456842e+02 0.344627 0.942836 0.125023 0.271112 39 3.174732 3.256988 3838 1.659312e+03 2.035670e+02 0.227284 0.974488 0.035789 0.164657 40 3.096450 3.174526 4121 1.301705e+03 1.822127e+02 0.149891 0.989708 0.005660 0.114564 41 3.021703 3.096237 4260 1.061902e+03 1.515946e+02 0.092668 0.995789 0.003837 0.068848 42 2.950747 3.021651 4516 7.914594e+02 1.274119e+02 0.036927 0.999748 0.012759 0.017619 43 2.882816 2.950388 4714 6.352505e+02 1.048061e+02 0.036500 0.999645 -0.001422 0.021943 44 2.818007 2.882637 4979 5.481048e+02 8.979147e+01 0.039295 0.999445 -0.024399 0.027370 45 2.756052 2.817944 5118 4.713274e+02 7.725465e+01 0.027187 0.999714 0.000814 0.024122 46 2.696815 2.756020 5470 4.034945e+02 6.438733e+01 0.009702 0.999857 0.004186 0.016334 47 2.640041 2.696761 5528 3.640797e+02 5.676994e+01 0.019257 0.999793 0.016699 0.017699 48 2.585573 2.640000 5993 3.224624e+02 4.945448e+01 0.023196 0.999936 -0.002423 0.007170 49 2.533415 2.585550 6045 2.929164e+02 4.222527e+01 0.003094 0.999992 0.033025 -0.002441 50 2.483177 2.533274 6405 2.715756e+02 3.649156e+01 0.002898 0.999972 0.016077 0.006600 51 2.434954 2.483107 6667 2.641690e+02 3.224973e+01 0.001402 0.999996 0.021569 0.005298 52 2.388588 2.434874 6994 2.433517e+02 2.856760e+01 -0.012759 0.999888 0.029843 -0.002527 53 2.343955 2.388571 7045 2.219761e+02 2.498505e+01 -0.031309 0.999658 0.022917 -0.020005 54 2.300921 2.343925 7468 2.085108e+02 2.131236e+01 -0.040401 0.999452 0.001985 -0.024730 55 2.259494 2.300866 7694 1.955098e+02 1.799082e+01 -0.040797 0.999405 -0.001459 -0.031318 56 2.219474 2.259458 7996 1.956897e+02 1.535406e+01 -0.034320 0.999704 -0.001907 -0.018373 57 2.200015 2.219456 4014 1.921935e+02 1.409081e+01 -0.016656 0.999989 0.004759 -0.005724 Map-model FSCaverages (at 3.00 A): FSCaverage(full) = 0.6053 Run loggraph refined_fsc.log to see plots. Starting Fo-Fc calculation.. with limited functionality because half maps were not provided model: refined.mmcif mask: not used WARNING: --sharpening_b=0.0 is given Setting blur= 46.19 in density calculation (unblurred later) Calculating Fc using Mott-Bethe formula done. Fc calculation time: 0.1 s Bin 1 only has 2 data. Merging with next bin. Bin 42 only has 1336 data. Merging with previous bin. Calculating maps.. sharpening method: 1/exp(-B*s^2/4) with B= 0.00 finished in 0.012 sec. Writing MTZ file: diffmap.mtz ============================================================================= * Final Summary * Rmsd from ideal bond lengths: 0.0080 A bond angles: 1.587 deg Map-model FSCaverages (at 3.00 A): FSCaverage(full) = 0.6053 Run loggraph refined_fsc.log to see plots ADP statistics Chain 0 ( 468 atoms) min= 26.2 median= 95.9 max=339.8 A^2 Chain 1 ( 371 atoms) min= 25.7 median= 74.6 max=317.8 A^2 Chain 2 ( 77 atoms) min= 62.2 median= 99.7 max=228.4 A^2 Chain 3 (1640 atoms) min= 25.6 median= 78.4 max=387.1 A^2 All (2556 atoms) min= 25.6 median= 81.4 max=387.1 A^2 Weight used: 1.96000004 If you want to change the weight, give larger (looser restraints) or smaller (tighter) value to --weight_auto_scale=. Open refined model and diffmap.mtz with COOT: coot --script refined_coot.py Open refined model, map and difference map with ChimeraX/ISOLDE: chimerax refined_chimerax.cxc WARNING: --mask_for_fofc was not given, so the Fo-Fc map was not normalized. ============================================================================= # Finished on 2024-08-12 12:50:20.870198