Starting phenix.real_space_refine on Wed Jun 11 05:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_31985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_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/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_31985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_31985.map" model { file = "/net/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_31985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh3_31985/06_2025/7vh3_31985.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.79, per 1000 atoms: 0.53 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 - 3.00 Amino acid : True - 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: 2.61 Conformation dependent library (CDL) restraints added in 1.5 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: 2.12 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: 5.21 Time building geometry restraints manager: 3.22 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: 0.00 - 3.39: 17173 3.39 - 6.79: 250 6.79 - 10.18: 57 10.18 - 13.57: 5 13.57 - 16.97: 2 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 3.040 nonbonded pdb=" O VAL A 770 " pdb=" OG SER A1363 " model vdw 2.304 3.040 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 3.040 nonbonded pdb=" OG SER A 121 " pdb=" OH TYR A 835 " model vdw 2.331 3.040 ... (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 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 Make a string to write initial .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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 12970 Z= 0.235 Angle : 1.095 16.966 17493 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 % Allowed : 6.45 % Favored : 92.64 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1680 HIS 0.008 0.002 HIS A 647 PHE 0.027 0.003 PHE A1386 TYR 0.026 0.002 TYR A 555 ARG 0.009 0.001 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.15572 ( 481) hydrogen bonds : angle 7.20007 ( 1395) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.53124 ( 6) covalent geometry : bond 0.00510 (12967) covalent geometry : angle 1.09453 (17487) *********************** 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 to be fit. rotamer outliers: 13 poor density : 416 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.6380 (t80) cc_final: 0.6062 (t80) REVERT: A 329 SER cc_start: 0.6708 (p) cc_final: 0.6332 (t) REVERT: A 376 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.6738 (mmm-85) REVERT: A 640 MET cc_start: 0.7231 (mtm) cc_final: 0.7015 (mtm) REVERT: A 652 ILE cc_start: 0.8361 (mm) cc_final: 0.8104 (mm) REVERT: A 714 LEU cc_start: 0.8133 (tt) cc_final: 0.7622 (mp) REVERT: A 1103 THR cc_start: 0.6834 (m) cc_final: 0.6528 (p) REVERT: A 1141 MET cc_start: 0.8557 (mmt) cc_final: 0.8101 (mmt) REVERT: A 1144 LEU cc_start: 0.8228 (mt) cc_final: 0.7965 (mt) REVERT: A 1162 ASN cc_start: 0.6247 (p0) cc_final: 0.5388 (m110) REVERT: A 1309 PHE cc_start: 0.6627 (t80) cc_final: 0.6363 (t80) REVERT: A 1321 ILE cc_start: 0.7757 (pt) cc_final: 0.7433 (tp) outliers start: 13 outliers final: 7 residues processed: 425 average time/residue: 0.2970 time to fit residues: 173.0461 Evaluate side-chains 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 1560 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS A 390 ASN A 472 HIS A 522 ASN A1114 ASN A1128 ASN A1154 ASN A1179 ASN A1241 ASN A1292 GLN A1297 ASN A1308 GLN A1331 GLN A1405 HIS A1665 ASN A1689 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.202676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.173738 restraints weight = 15423.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171452 restraints weight = 15190.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.172705 restraints weight = 15112.065| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12970 Z= 0.162 Angle : 0.709 13.157 17493 Z= 0.361 Chirality : 0.044 0.170 2015 Planarity : 0.005 0.043 2209 Dihedral : 6.588 59.992 1728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 3.75 % Allowed : 13.39 % Favored : 82.86 % 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: -3.45 (0.18), residues: 1582 helix: -1.67 (0.16), residues: 744 sheet: -3.83 (0.45), residues: 70 loop : -2.77 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1230 HIS 0.003 0.001 HIS A 647 PHE 0.025 0.002 PHE A1148 TYR 0.016 0.002 TYR A 835 ARG 0.006 0.001 ARG A1796 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 481) hydrogen bonds : angle 5.07597 ( 1395) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.93067 ( 6) covalent geometry : bond 0.00359 (12967) covalent geometry : angle 0.70878 (17487) *********************** 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 298 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.7159 (p) cc_final: 0.6767 (t) REVERT: A 527 GLU cc_start: 0.7452 (pp20) cc_final: 0.6450 (pm20) REVERT: A 714 LEU cc_start: 0.8279 (tt) cc_final: 0.7610 (mp) REVERT: A 741 ASN cc_start: 0.7093 (p0) cc_final: 0.6862 (p0) REVERT: A 781 ASN cc_start: 0.8400 (t0) cc_final: 0.8200 (m-40) REVERT: A 848 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6924 (ttm) REVERT: A 1021 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 1141 MET cc_start: 0.8767 (mmt) cc_final: 0.8258 (mmt) REVERT: A 1162 ASN cc_start: 0.6232 (p0) cc_final: 0.5480 (m110) REVERT: A 1290 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: A 1312 TYR cc_start: 0.7431 (t80) cc_final: 0.7229 (t80) REVERT: A 1321 ILE cc_start: 0.7953 (pt) cc_final: 0.7590 (tp) REVERT: A 1355 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 1375 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (mt) REVERT: A 1663 TYR cc_start: 0.6751 (m-80) cc_final: 0.6229 (m-10) outliers start: 54 outliers final: 24 residues processed: 280 average time/residue: 0.2327 time to fit residues: 96.9361 Evaluate side-chains 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1805 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 197 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 ASN A1292 GLN A1358 HIS A1478 GLN A1689 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.197223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167123 restraints weight = 15770.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164896 restraints weight = 15905.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166133 restraints weight = 15976.761| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12970 Z= 0.178 Angle : 0.701 9.386 17493 Z= 0.355 Chirality : 0.044 0.180 2015 Planarity : 0.004 0.048 2209 Dihedral : 6.218 54.521 1725 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.36 % Favored : 90.58 % Rotamer: Outliers : 4.79 % Allowed : 15.20 % Favored : 80.01 % 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: -2.83 (0.20), residues: 1582 helix: -1.10 (0.17), residues: 757 sheet: -4.34 (0.40), residues: 61 loop : -2.48 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1230 HIS 0.005 0.001 HIS A 647 PHE 0.030 0.002 PHE A 352 TYR 0.024 0.002 TYR A 555 ARG 0.007 0.001 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 481) hydrogen bonds : angle 4.79083 ( 1395) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.87617 ( 6) covalent geometry : bond 0.00417 (12967) covalent geometry : angle 0.70088 (17487) *********************** 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 289 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 220 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6939 (mm) REVERT: A 224 ILE cc_start: 0.8387 (pt) cc_final: 0.8029 (tt) REVERT: A 329 SER cc_start: 0.7287 (p) cc_final: 0.6882 (t) REVERT: A 376 ARG cc_start: 0.7160 (mmm-85) cc_final: 0.6664 (mmm-85) REVERT: A 714 LEU cc_start: 0.8335 (tt) cc_final: 0.7687 (mp) REVERT: A 848 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7194 (ttm) REVERT: A 1021 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 1030 TYR cc_start: 0.7809 (m-10) cc_final: 0.7378 (m-80) REVERT: A 1141 MET cc_start: 0.8782 (mmt) cc_final: 0.8289 (mmt) REVERT: A 1162 ASN cc_start: 0.6497 (p0) cc_final: 0.6014 (m-40) REVERT: A 1290 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6608 (tmm) REVERT: A 1321 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 1355 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7290 (mm) REVERT: A 1438 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7462 (mtt180) REVERT: A 1662 ILE cc_start: 0.6695 (mm) cc_final: 0.6447 (mm) REVERT: A 1663 TYR cc_start: 0.6885 (m-80) cc_final: 0.6311 (m-10) outliers start: 69 outliers final: 41 residues processed: 266 average time/residue: 0.2501 time to fit residues: 98.3357 Evaluate side-chains 242 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.1881 > 50: distance: 46 - 51: 17.327 distance: 51 - 52: 20.366 distance: 52 - 53: 18.834 distance: 52 - 55: 18.917 distance: 53 - 54: 26.699 distance: 53 - 62: 37.742 distance: 55 - 56: 13.602 distance: 56 - 57: 9.038 distance: 56 - 58: 6.789 distance: 57 - 59: 17.059 distance: 58 - 60: 19.374 distance: 59 - 61: 10.869 distance: 62 - 63: 18.550 distance: 63 - 64: 25.033 distance: 63 - 66: 8.730 distance: 64 - 65: 14.040 distance: 64 - 73: 17.887 distance: 66 - 67: 4.500 distance: 67 - 68: 15.700 distance: 67 - 69: 12.895 distance: 68 - 70: 18.086 distance: 69 - 71: 13.228 distance: 71 - 72: 7.914 distance: 73 - 74: 4.903 distance: 73 - 177: 6.817 distance: 74 - 75: 11.082 distance: 74 - 77: 11.173 distance: 75 - 76: 4.523 distance: 75 - 87: 7.389 distance: 76 - 174: 9.339 distance: 78 - 79: 3.253 distance: 80 - 82: 3.708 distance: 81 - 82: 4.187 distance: 87 - 88: 7.914 distance: 88 - 89: 11.190 distance: 88 - 91: 10.487 distance: 89 - 90: 16.480 distance: 89 - 92: 12.818 distance: 92 - 93: 12.150 distance: 93 - 94: 29.352 distance: 93 - 96: 24.231 distance: 94 - 95: 20.696 distance: 94 - 99: 15.188 distance: 96 - 97: 9.294 distance: 96 - 98: 33.556 distance: 99 - 100: 12.563 distance: 100 - 101: 24.844 distance: 100 - 103: 9.197 distance: 101 - 102: 7.176 distance: 101 - 108: 12.184 distance: 103 - 104: 14.199 distance: 104 - 105: 17.882 distance: 105 - 106: 36.733 distance: 106 - 107: 10.683 distance: 108 - 114: 23.930 distance: 109 - 110: 4.575 distance: 109 - 112: 7.332 distance: 110 - 111: 15.992 distance: 110 - 115: 8.294 distance: 112 - 113: 17.807 distance: 113 - 114: 5.139 distance: 115 - 116: 9.902 distance: 116 - 117: 11.819 distance: 116 - 119: 17.269 distance: 117 - 118: 10.018 distance: 117 - 124: 30.202 distance: 119 - 120: 6.773 distance: 120 - 121: 8.146 distance: 121 - 122: 6.858 distance: 122 - 123: 8.248 distance: 124 - 125: 14.897 distance: 125 - 126: 40.249 distance: 125 - 128: 19.035 distance: 126 - 127: 33.272 distance: 126 - 131: 23.190 distance: 128 - 129: 7.037 distance: 128 - 130: 13.802 distance: 131 - 132: 19.081 distance: 132 - 133: 3.693 distance: 132 - 135: 13.128 distance: 133 - 134: 11.178 distance: 133 - 138: 12.315 distance: 135 - 136: 12.506 distance: 135 - 137: 7.909