Starting phenix.real_space_refine (version: 1.20rc2) on Tue Nov 2 09:22:20 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/11_2021/7vh3_31985.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1591": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1741": "NH1" <-> "NH2" Residue "A ARG 1796": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc2-4405/modules/chem_data/mon_lib" Total number of atoms: 12749 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Time building chain proxies: 6.91, per 1000 atoms: 0.54 Number of scatterers: 12749 At special positions: 0 Unit cell: (113.98, 109.06, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2389 8.00 N 2129 7.00 C 8144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1650 " - pdb=" SG CYS A1664 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 48.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.722A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.888A pdb=" N ALA A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.650A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.268A pdb=" N SER A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 108 through 125 removed outlier: 4.100A pdb=" N GLU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 164 through 175 removed outlier: 4.294A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.535A pdb=" N ASN A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.589A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.799A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.909A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.907A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 5.573A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.849A pdb=" N ARG A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.662A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.790A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'A' and resid 602 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 626 through 644 removed outlier: 4.011A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 637 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.946A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.953A pdb=" N VAL A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 713 through 732 removed outlier: 3.630A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 788 Processing helix chain 'A' and resid 835 through 852 removed outlier: 4.437A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 Processing helix chain 'A' and resid 887 through 895 removed outlier: 4.530A pdb=" N MET A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 918 Processing helix chain 'A' and resid 961 through 969 removed outlier: 3.730A pdb=" N ASP A 969 " --> pdb=" O HIS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1024 through 1033 Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 4.148A pdb=" N LEU A1091 " --> pdb=" O ASN A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1156 removed outlier: 3.866A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1181 removed outlier: 3.587A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.996A pdb=" N MET A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.659A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 4.577A pdb=" N ILE A1227 " --> pdb=" O SER A1223 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A1230 " --> pdb=" O SER A1226 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1273 Processing helix chain 'A' and resid 1295 through 1318 removed outlier: 3.611A pdb=" N TYR A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.584A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 4.204A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1428 removed outlier: 3.592A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1450 removed outlier: 3.568A pdb=" N SER A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 3.534A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 3.879A pdb=" N ILE A1519 " --> pdb=" O LEU A1515 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1515 through 1520' Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.970A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 Processing helix chain 'A' and resid 1614 through 1624 removed outlier: 3.650A pdb=" N GLY A1620 " --> pdb=" O SER A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1646 removed outlier: 3.539A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A1646 " --> pdb=" O GLU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1692 Processing helix chain 'A' and resid 1743 through 1750 removed outlier: 3.590A pdb=" N GLU A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.735A pdb=" N MET A1781 " --> pdb=" O ILE A1777 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1777 through 1782' Processing helix chain 'A' and resid 1788 through 1792 removed outlier: 3.886A pdb=" N HIS A1791 " --> pdb=" O ILE A1788 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.517A pdb=" N THR A 94 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.849A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 559 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 566 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 459 removed outlier: 3.557A pdb=" N VAL A 523 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA6, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.729A pdb=" N GLU A1237 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 3.518A pdb=" N LEU A1183 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB1, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AB2, first strand: chain 'A' and resid 1716 through 1718 481 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3714 1.34 - 1.46: 2395 1.46 - 1.58: 6731 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 12967 Sorted by residual: bond pdb=" CA LEU A1288 " pdb=" CB LEU A1288 " ideal model delta sigma weight residual 1.525 1.554 -0.030 1.25e-02 6.40e+03 5.72e+00 bond pdb=" C LEU A 580 " pdb=" N PRO A 581 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 bond pdb=" CB ASN A 344 " pdb=" CG ASN A 344 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.37e+00 bond pdb=" CA SER A 950 " pdb=" C SER A 950 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.50e+00 bond pdb=" CB PHE A1386 " pdb=" CG PHE A1386 " ideal model delta sigma weight residual 1.502 1.538 -0.036 2.30e-02 1.89e+03 2.48e+00 ... (remaining 12962 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.62: 161 104.62 - 111.98: 5875 111.98 - 119.34: 4842 119.34 - 126.71: 6468 126.71 - 134.07: 141 Bond angle restraints: 17487 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 109.34 126.31 -16.97 2.08e+00 2.31e-01 6.65e+01 angle pdb=" N LEU A 388 " pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 108.19 117.45 -9.26 1.29e+00 6.01e-01 5.15e+01 angle pdb=" N VAL A 389 " pdb=" CA VAL A 389 " pdb=" C VAL A 389 " ideal model delta sigma weight residual 109.34 122.95 -13.61 2.08e+00 2.31e-01 4.28e+01 angle pdb=" C LEU A 260 " pdb=" N THR A 261 " pdb=" CA THR A 261 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C LEU A1365 " pdb=" N ASN A1366 " pdb=" CA ASN A1366 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 ... (remaining 17482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 7286 15.42 - 30.84: 482 30.84 - 46.26: 119 46.26 - 61.68: 10 61.68 - 77.11: 7 Dihedral angle restraints: 7904 sinusoidal: 3187 harmonic: 4717 Sorted by residual: dihedral pdb=" CA LEU A 702 " pdb=" C LEU A 702 " pdb=" N CYS A 703 " pdb=" CA CYS A 703 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLY A1694 " pdb=" C GLY A1694 " pdb=" N GLU A1695 " pdb=" CA GLU A1695 " ideal model delta harmonic sigma weight residual -180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA THR A 710 " pdb=" C THR A 710 " pdb=" N PRO A 711 " pdb=" CA PRO A 711 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1639 0.070 - 0.140: 323 0.140 - 0.210: 37 0.210 - 0.280: 12 0.280 - 0.350: 4 Chirality restraints: 2015 Sorted by residual: chirality pdb=" CA ILE A 396 " pdb=" N ILE A 396 " pdb=" C ILE A 396 " pdb=" CB ILE A 396 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB ILE A1510 " pdb=" CA ILE A1510 " pdb=" CG1 ILE A1510 " pdb=" CG2 ILE A1510 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA VAL A 389 " pdb=" N VAL A 389 " pdb=" C VAL A 389 " pdb=" CB VAL A 389 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2012 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1290 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C MET A1290 " 0.052 2.00e-02 2.50e+03 pdb=" O MET A1290 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A1291 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 950 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO A 951 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 951 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 951 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 261 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C THR A 261 " -0.041 2.00e-02 2.50e+03 pdb=" O THR A 261 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 262 " 0.014 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2918 2.79 - 3.31: 11783 3.31 - 3.84: 20916 3.84 - 4.37: 24168 4.37 - 4.90: 40430 Nonbonded interactions: 100215 Sorted by model distance: nonbonded pdb=" OG SER A1098 " pdb=" OG SER A1101 " model vdw 2.257 2.440 nonbonded pdb=" O VAL A 770 " pdb=" OG SER A1363 " model vdw 2.304 2.440 nonbonded pdb=" CG2 VAL A1001 " pdb=" N LEU A1002 " model vdw 2.314 3.540 nonbonded pdb=" O GLU A1695 " pdb=" OG SER A1816 " model vdw 2.324 2.440 nonbonded pdb=" OG SER A 121 " pdb=" OH TYR A 835 " model vdw 2.331 2.440 ... (remaining 100210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8144 2.51 5 N 2129 2.21 5 O 2389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 35.620 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 12967 Z= 0.334 Angle : 1.095 16.966 17487 Z= 0.579 Chirality : 0.059 0.350 2015 Planarity : 0.007 0.061 2209 Dihedral : 11.491 77.105 4825 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.53 % Favored : 91.02 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.16), residues: 1582 helix: -3.10 (0.12), residues: 731 sheet: -3.82 (0.48), residues: 67 loop : -3.26 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 416 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 425 average time/residue: 0.2861 time to fit residues: 167.6900 Evaluate side-chains 226 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 219 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1277 time to fit residues: 3.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 HIS A 63 ASN A 131 GLN A 148 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 472 HIS A 522 ASN A 906 ASN A1114 ASN A1128 ASN A1154 ASN A1179 ASN A1241 ASN A1297 ASN A1308 GLN A1331 GLN A1405 HIS A1665 ASN A1689 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 12967 Z= 0.200 Angle : 0.680 13.786 17487 Z= 0.340 Chirality : 0.043 0.375 2015 Planarity : 0.005 0.087 2209 Dihedral : 5.643 34.660 1716 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.19), residues: 1582 helix: -1.45 (0.17), residues: 747 sheet: -3.77 (0.53), residues: 52 loop : -2.81 (0.20), residues: 783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 246 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 22 residues processed: 286 average time/residue: 0.2353 time to fit residues: 100.0259 Evaluate side-chains 218 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1168 time to fit residues: 7.0473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A 859 ASN A1088 ASN A1111 ASN A1358 HIS A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 12967 Z= 0.234 Angle : 0.665 9.257 17487 Z= 0.333 Chirality : 0.044 0.414 2015 Planarity : 0.004 0.082 2209 Dihedral : 5.376 34.330 1716 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1582 helix: -0.78 (0.18), residues: 755 sheet: -3.74 (0.42), residues: 72 loop : -2.48 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 239 average time/residue: 0.2498 time to fit residues: 88.4354 Evaluate side-chains 207 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1193 time to fit residues: 6.6889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 0.0270 chunk 139 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 206 HIS A 288 ASN A 384 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.083 12967 Z= 0.160 Angle : 0.625 14.370 17487 Z= 0.311 Chirality : 0.041 0.313 2015 Planarity : 0.004 0.044 2209 Dihedral : 4.893 32.683 1716 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1582 helix: -0.21 (0.19), residues: 753 sheet: -3.30 (0.44), residues: 79 loop : -2.31 (0.22), residues: 750 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 244 average time/residue: 0.2709 time to fit residues: 95.4579 Evaluate side-chains 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1298 time to fit residues: 4.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1162 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 12967 Z= 0.265 Angle : 0.694 14.951 17487 Z= 0.348 Chirality : 0.044 0.440 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.161 34.686 1716 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.02 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.21), residues: 1582 helix: -0.18 (0.19), residues: 755 sheet: -3.44 (0.45), residues: 72 loop : -2.21 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 1.569 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 233 average time/residue: 0.2363 time to fit residues: 81.2072 Evaluate side-chains 206 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1522 time to fit residues: 6.6584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 129 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 12967 Z= 0.192 Angle : 0.645 16.419 17487 Z= 0.325 Chirality : 0.042 0.389 2015 Planarity : 0.004 0.044 2209 Dihedral : 4.788 33.161 1716 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1582 helix: 0.15 (0.19), residues: 754 sheet: -3.17 (0.46), residues: 77 loop : -2.16 (0.22), residues: 751 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.501 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 222 average time/residue: 0.2282 time to fit residues: 76.0718 Evaluate side-chains 197 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1427 time to fit residues: 5.0035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 12967 Z= 0.185 Angle : 0.607 9.614 17487 Z= 0.307 Chirality : 0.041 0.349 2015 Planarity : 0.004 0.105 2209 Dihedral : 4.562 31.535 1716 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.59 % Favored : 92.35 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1582 helix: 0.42 (0.19), residues: 749 sheet: -2.98 (0.47), residues: 76 loop : -2.09 (0.22), residues: 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.535 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 216 average time/residue: 0.2490 time to fit residues: 80.9129 Evaluate side-chains 189 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1364 time to fit residues: 3.1090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 121 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 12967 Z= 0.231 Angle : 0.656 10.275 17487 Z= 0.329 Chirality : 0.043 0.334 2015 Planarity : 0.004 0.077 2209 Dihedral : 4.751 34.519 1716 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.78 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1582 helix: 0.33 (0.19), residues: 749 sheet: -3.12 (0.47), residues: 76 loop : -1.99 (0.23), residues: 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.557 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 191 average time/residue: 0.2353 time to fit residues: 67.5886 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1548 time to fit residues: 4.7643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 94 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.019 12967 Z= 0.644 Angle : 0.959 81.147 17487 Z= 0.434 Chirality : 0.044 0.322 2015 Planarity : 0.004 0.044 2209 Dihedral : 4.769 33.869 1716 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.72 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1582 helix: 0.33 (0.19), residues: 762 sheet: -3.07 (0.47), residues: 76 loop : -1.97 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 197 average time/residue: 0.2491 time to fit residues: 72.9782 Evaluate side-chains 183 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1292 time to fit residues: 3.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 160 optimal weight: 9.9990 chunk 147 optimal weight: 0.0980 chunk 127 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 78 optimal weight: 0.0370 chunk 101 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.080 12967 Z= 0.630 Angle : 1.041 97.791 17487 Z= 0.450 Chirality : 0.043 0.456 2015 Planarity : 0.004 0.075 2209 Dihedral : 4.664 33.506 1716 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.40 % Favored : 92.54 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1582 helix: 0.46 (0.19), residues: 755 sheet: -3.67 (0.52), residues: 56 loop : -1.87 (0.23), residues: 771 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 191 average time/residue: 0.2353 time to fit residues: 67.9377 Evaluate side-chains 182 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2232 time to fit residues: 3.2140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 7 optimal weight: 0.0050 chunk 92 optimal weight: 40.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.200756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170201 restraints weight = 16269.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169693 restraints weight = 16912.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.171587 restraints weight = 15294.129| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.061 12967 Z= 0.608 Angle : 1.089 106.095 17487 Z= 0.461 Chirality : 0.044 0.370 2015 Planarity : 0.005 0.110 2209 Dihedral : 4.674 33.168 1716 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.65 % Favored : 92.29 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1582 helix: 0.44 (0.19), residues: 757 sheet: -3.44 (0.51), residues: 58 loop : -1.90 (0.23), residues: 767 =============================================================================== Job complete usr+sys time: 2572.78 seconds wall clock time: 47 minutes 54.27 seconds (2874.27 seconds total)