Starting phenix.real_space_refine on Thu Sep 26 07:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/09_2024/7vh3_31985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/09_2024/7vh3_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_31985/09_2024/7vh3_31985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/09_2024/7vh3_31985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/09_2024/7vh3_31985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/09_2024/7vh3_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.39, per 1000 atoms: 0.58 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: 2.51 Conformation dependent library (CDL) restraints added in 1.6 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: 1.49 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: 4.52 Time building geometry restraints manager: 3.04 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: 0.010 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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 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 % 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 *********************** 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 : 1.529 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: 0.2980 time to fit residues: 174.0795 Evaluate side-chains 232 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 12967 Z= 0.232 Angle : 0.709 13.157 17487 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 *********************** 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 fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.6663 (p) cc_final: 0.6267 (t) REVERT: A 527 GLU cc_start: 0.7282 (pp20) cc_final: 0.6453 (pm20) REVERT: A 714 LEU cc_start: 0.8180 (tt) cc_final: 0.7574 (mp) REVERT: A 741 ASN cc_start: 0.6822 (p0) cc_final: 0.6546 (p0) REVERT: A 848 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6542 (ttm) REVERT: A 1141 MET cc_start: 0.8659 (mmt) cc_final: 0.8193 (mmt) REVERT: A 1162 ASN cc_start: 0.6060 (p0) cc_final: 0.5420 (m110) REVERT: A 1290 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6749 (tmm) REVERT: A 1312 TYR cc_start: 0.7198 (t80) cc_final: 0.6994 (t80) REVERT: A 1321 ILE cc_start: 0.7697 (pt) cc_final: 0.7408 (tp) REVERT: A 1355 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7147 (mm) REVERT: A 1375 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 1663 TYR cc_start: 0.6559 (m-80) cc_final: 0.6112 (m-10) outliers start: 54 outliers final: 24 residues processed: 280 average time/residue: 0.2351 time to fit residues: 97.1582 Evaluate side-chains 218 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 81 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 906 ASN A1034 GLN A1292 GLN ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1478 GLN A1665 ASN A1689 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12967 Z= 0.389 Angle : 0.786 10.573 17487 Z= 0.400 Chirality : 0.047 0.204 2015 Planarity : 0.005 0.053 2209 Dihedral : 6.545 50.438 1725 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.48 % Favored : 90.46 % Rotamer: Outliers : 5.07 % Allowed : 15.75 % Favored : 79.18 % 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: -3.07 (0.19), residues: 1582 helix: -1.35 (0.17), residues: 766 sheet: -3.81 (0.41), residues: 81 loop : -2.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1230 HIS 0.006 0.002 HIS A1358 PHE 0.028 0.003 PHE A 352 TYR 0.028 0.002 TYR A 555 ARG 0.007 0.001 ARG A 376 *********************** 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 302 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 229 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 714 LEU cc_start: 0.8335 (tt) cc_final: 0.7687 (mp) REVERT: A 848 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6876 (ttm) REVERT: A 1030 TYR cc_start: 0.8099 (m-10) cc_final: 0.7700 (m-80) REVERT: A 1141 MET cc_start: 0.8675 (mmt) cc_final: 0.8241 (mmt) REVERT: A 1162 ASN cc_start: 0.6954 (p0) cc_final: 0.6499 (m110) REVERT: A 1219 ILE cc_start: 0.7270 (pt) cc_final: 0.7046 (pt) REVERT: A 1240 ILE cc_start: 0.8355 (tp) cc_final: 0.8154 (tt) REVERT: A 1321 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7576 (tp) REVERT: A 1355 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 1578 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7168 (m) REVERT: A 1662 ILE cc_start: 0.6962 (mm) cc_final: 0.6736 (mm) outliers start: 73 outliers final: 44 residues processed: 276 average time/residue: 0.2576 time to fit residues: 102.6651 Evaluate side-chains 240 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 85 LYS 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 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 757 LYS 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 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER 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 1433 THR Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1578 VAL 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 ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1358 HIS A1665 ASN A1805 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12967 Z= 0.186 Angle : 0.659 10.636 17487 Z= 0.332 Chirality : 0.042 0.157 2015 Planarity : 0.004 0.042 2209 Dihedral : 5.794 49.608 1723 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.16 % Rotamer: Outliers : 4.86 % Allowed : 17.14 % Favored : 78.00 % 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: -2.30 (0.20), residues: 1582 helix: -0.55 (0.18), residues: 762 sheet: -3.58 (0.44), residues: 79 loop : -2.35 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1230 HIS 0.004 0.001 HIS A 647 PHE 0.027 0.002 PHE A1148 TYR 0.016 0.002 TYR A 555 ARG 0.007 0.001 ARG A 376 *********************** 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 295 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 225 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7089 (mm) REVERT: A 714 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 728 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7028 (ttmp) REVERT: A 838 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: A 848 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6770 (ttm) REVERT: A 1030 TYR cc_start: 0.7972 (m-10) cc_final: 0.7701 (m-80) REVERT: A 1141 MET cc_start: 0.8572 (mmt) cc_final: 0.8187 (mmt) REVERT: A 1290 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6425 (tmm) REVERT: A 1385 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: A 1434 LYS cc_start: 0.7493 (tttm) cc_final: 0.6831 (tttt) outliers start: 70 outliers final: 37 residues processed: 276 average time/residue: 0.2447 time to fit residues: 99.2588 Evaluate side-chains 231 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 282 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 838 GLU 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 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1247 CYS 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 1354 MET Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1385 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 139 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 335 ASN A 449 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12967 Z= 0.214 Angle : 0.657 9.977 17487 Z= 0.332 Chirality : 0.043 0.169 2015 Planarity : 0.004 0.078 2209 Dihedral : 5.649 40.033 1723 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer: Outliers : 4.51 % Allowed : 18.81 % Favored : 76.68 % 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: -1.97 (0.21), residues: 1582 helix: -0.19 (0.19), residues: 752 sheet: -3.66 (0.46), residues: 75 loop : -2.24 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.004 0.001 HIS A 647 PHE 0.023 0.002 PHE A 352 TYR 0.015 0.002 TYR A 572 ARG 0.007 0.001 ARG A 376 *********************** 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 271 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 206 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 714 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 741 ASN cc_start: 0.6835 (p0) cc_final: 0.6593 (p0) REVERT: A 838 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: A 848 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6649 (ttm) REVERT: A 869 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7484 (mt) REVERT: A 870 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6874 (tt) REVERT: A 1141 MET cc_start: 0.8551 (mmt) cc_final: 0.8170 (mmt) REVERT: A 1290 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6533 (tmm) REVERT: A 1321 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7419 (tp) REVERT: A 1385 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7688 (mtp180) REVERT: A 1434 LYS cc_start: 0.7307 (tttm) cc_final: 0.6911 (tttm) REVERT: A 1438 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7459 (mtt180) REVERT: A 1781 MET cc_start: 0.4735 (mmm) cc_final: 0.3289 (ppp) outliers start: 65 outliers final: 41 residues processed: 250 average time/residue: 0.2322 time to fit residues: 86.2067 Evaluate side-chains 243 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 224 ILE 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 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 838 GLU 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 860 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER 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 1375 ILE Chi-restraints excluded: chain A residue 1385 ARG 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 1614 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 449 GLN A 859 ASN A1034 GLN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12967 Z= 0.182 Angle : 0.629 9.136 17487 Z= 0.318 Chirality : 0.042 0.164 2015 Planarity : 0.004 0.058 2209 Dihedral : 5.425 43.682 1723 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.79 % Rotamer: Outliers : 4.16 % Allowed : 19.29 % Favored : 76.54 % 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: -1.73 (0.21), residues: 1582 helix: 0.04 (0.19), residues: 759 sheet: -3.87 (0.50), residues: 61 loop : -2.20 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.004 0.001 HIS A 647 PHE 0.019 0.001 PHE A1025 TYR 0.021 0.001 TYR A1030 ARG 0.007 0.000 ARG A 376 *********************** 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 277 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7068 (mm) REVERT: A 329 SER cc_start: 0.6677 (m) cc_final: 0.6322 (t) REVERT: A 485 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7489 (tpt170) REVERT: A 573 CYS cc_start: 0.6125 (t) cc_final: 0.5735 (m) REVERT: A 696 LEU cc_start: 0.8505 (mt) cc_final: 0.8291 (mt) REVERT: A 714 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7695 (mp) REVERT: A 848 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6522 (ttm) REVERT: A 870 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6954 (tt) REVERT: A 1141 MET cc_start: 0.8564 (mmt) cc_final: 0.8158 (mmt) REVERT: A 1230 TRP cc_start: 0.7569 (m-10) cc_final: 0.7291 (m-10) REVERT: A 1290 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6357 (tmm) REVERT: A 1321 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 1385 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7622 (mtp180) REVERT: A 1781 MET cc_start: 0.4594 (mmm) cc_final: 0.3329 (ppp) outliers start: 60 outliers final: 40 residues processed: 258 average time/residue: 0.2311 time to fit residues: 88.3741 Evaluate side-chains 237 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 282 SER 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 436 ILE Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ASP 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 1242 VAL 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 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1385 ARG 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 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 0.0060 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 0.0060 chunk 97 optimal weight: 0.0470 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.3912 ------------------------------------------------------------------------------- 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 800 ASN A 859 ASN A 872 ASN A1034 GLN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12967 Z= 0.166 Angle : 0.636 9.691 17487 Z= 0.317 Chirality : 0.042 0.159 2015 Planarity : 0.004 0.045 2209 Dihedral : 5.301 46.964 1723 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 3.89 % Allowed : 19.99 % Favored : 76.13 % 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: -1.52 (0.21), residues: 1582 helix: 0.26 (0.19), residues: 752 sheet: -3.98 (0.53), residues: 56 loop : -2.11 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1549 HIS 0.004 0.001 HIS A 647 PHE 0.033 0.001 PHE A 352 TYR 0.015 0.001 TYR A 572 ARG 0.010 0.000 ARG A 376 *********************** 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 265 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7065 (mm) REVERT: A 329 SER cc_start: 0.6633 (m) cc_final: 0.6338 (t) REVERT: A 485 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7475 (tpt170) REVERT: A 573 CYS cc_start: 0.6055 (t) cc_final: 0.5673 (m) REVERT: A 696 LEU cc_start: 0.8422 (mt) cc_final: 0.8183 (mt) REVERT: A 714 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 1120 SER cc_start: 0.6696 (OUTLIER) cc_final: 0.6353 (p) REVERT: A 1141 MET cc_start: 0.8553 (mmt) cc_final: 0.8132 (mmt) REVERT: A 1230 TRP cc_start: 0.7548 (m-10) cc_final: 0.7298 (m-10) REVERT: A 1290 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6278 (tmm) REVERT: A 1321 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7130 (tp) REVERT: A 1385 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: A 1780 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5884 (t70) outliers start: 56 outliers final: 34 residues processed: 247 average time/residue: 0.2343 time to fit residues: 86.4684 Evaluate side-chains 236 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 282 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER 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 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 0.0470 chunk 121 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 chunk 148 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.6884 ------------------------------------------------------------------------------- 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 748 GLN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12967 Z= 0.180 Angle : 0.644 9.588 17487 Z= 0.321 Chirality : 0.042 0.216 2015 Planarity : 0.004 0.045 2209 Dihedral : 5.014 34.572 1719 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.33 % Allowed : 20.47 % Favored : 76.20 % 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: -1.48 (0.21), residues: 1582 helix: 0.33 (0.19), residues: 749 sheet: -3.89 (0.49), residues: 62 loop : -2.12 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1549 HIS 0.004 0.001 HIS A 647 PHE 0.023 0.001 PHE A 693 TYR 0.015 0.001 TYR A 910 ARG 0.010 0.000 ARG A 376 *********************** 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 251 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7077 (mm) REVERT: A 329 SER cc_start: 0.6674 (m) cc_final: 0.6337 (t) REVERT: A 485 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7448 (tpt170) REVERT: A 573 CYS cc_start: 0.6060 (t) cc_final: 0.5670 (m) REVERT: A 696 LEU cc_start: 0.8495 (mt) cc_final: 0.8253 (mt) REVERT: A 714 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 869 ILE cc_start: 0.8666 (mt) cc_final: 0.8325 (mm) REVERT: A 1120 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6424 (p) REVERT: A 1141 MET cc_start: 0.8552 (mmt) cc_final: 0.8130 (mmt) REVERT: A 1230 TRP cc_start: 0.7522 (m-10) cc_final: 0.7281 (m-10) REVERT: A 1290 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6209 (tmm) REVERT: A 1321 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7124 (tp) REVERT: A 1385 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7578 (mtp180) REVERT: A 1472 SER cc_start: 0.9050 (m) cc_final: 0.8472 (t) REVERT: A 1780 ASP cc_start: 0.6059 (OUTLIER) cc_final: 0.5530 (t70) outliers start: 48 outliers final: 38 residues processed: 240 average time/residue: 0.2419 time to fit residues: 86.3063 Evaluate side-chains 238 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 282 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER 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 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 859 ASN A1405 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12967 Z= 0.195 Angle : 0.650 9.711 17487 Z= 0.328 Chirality : 0.043 0.214 2015 Planarity : 0.004 0.045 2209 Dihedral : 4.996 35.807 1719 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.89 % Allowed : 20.19 % Favored : 75.92 % 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: -1.48 (0.21), residues: 1582 helix: 0.33 (0.19), residues: 750 sheet: -3.89 (0.50), residues: 62 loop : -2.13 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1549 HIS 0.004 0.001 HIS A 647 PHE 0.026 0.001 PHE A 352 TYR 0.016 0.001 TYR A 572 ARG 0.009 0.000 ARG A 376 *********************** 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 254 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 198 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7085 (mm) REVERT: A 329 SER cc_start: 0.6645 (m) cc_final: 0.6300 (t) REVERT: A 485 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7479 (tpt170) REVERT: A 573 CYS cc_start: 0.6080 (t) cc_final: 0.5728 (m) REVERT: A 714 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 728 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6757 (ttmp) REVERT: A 869 ILE cc_start: 0.8614 (mt) cc_final: 0.8286 (mm) REVERT: A 988 TYR cc_start: 0.4185 (t80) cc_final: 0.3884 (t80) REVERT: A 1120 SER cc_start: 0.6691 (OUTLIER) cc_final: 0.6398 (p) REVERT: A 1141 MET cc_start: 0.8555 (mmt) cc_final: 0.8129 (mmt) REVERT: A 1230 TRP cc_start: 0.7536 (m-10) cc_final: 0.7284 (m-10) REVERT: A 1290 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6171 (tmm) REVERT: A 1321 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 1385 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7607 (mtp180) REVERT: A 1472 SER cc_start: 0.9059 (m) cc_final: 0.8447 (t) REVERT: A 1780 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5421 (t70) outliers start: 56 outliers final: 42 residues processed: 240 average time/residue: 0.2332 time to fit residues: 83.8712 Evaluate side-chains 237 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER 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 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER 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 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 160 optimal weight: 0.0020 chunk 147 optimal weight: 0.1980 chunk 127 optimal weight: 0.0060 chunk 13 optimal weight: 0.0010 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 0.1410 ------------------------------------------------------------------------------- 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 859 ASN A1791 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12967 Z= 0.166 Angle : 0.650 9.415 17487 Z= 0.328 Chirality : 0.042 0.206 2015 Planarity : 0.004 0.046 2209 Dihedral : 4.870 33.422 1719 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.19 % Allowed : 21.10 % Favored : 75.71 % 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: -1.30 (0.21), residues: 1582 helix: 0.46 (0.19), residues: 752 sheet: -3.77 (0.52), residues: 56 loop : -2.03 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1549 HIS 0.004 0.001 HIS A 647 PHE 0.015 0.001 PHE A 693 TYR 0.017 0.001 TYR A 910 ARG 0.007 0.000 ARG A1495 ********************** 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 250 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7055 (mm) REVERT: A 329 SER cc_start: 0.6593 (m) cc_final: 0.6295 (t) REVERT: A 485 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7432 (tpt170) REVERT: A 573 CYS cc_start: 0.5763 (t) cc_final: 0.5551 (m) REVERT: A 714 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 728 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6751 (ttmp) REVERT: A 869 ILE cc_start: 0.8579 (mt) cc_final: 0.8341 (mm) REVERT: A 1141 MET cc_start: 0.8520 (mmt) cc_final: 0.8084 (mmt) REVERT: A 1230 TRP cc_start: 0.7487 (m-10) cc_final: 0.7220 (m-10) REVERT: A 1290 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6037 (tmm) REVERT: A 1321 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7047 (tp) REVERT: A 1385 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: A 1780 ASP cc_start: 0.5702 (OUTLIER) cc_final: 0.5255 (t70) REVERT: A 1781 MET cc_start: 0.4648 (mmm) cc_final: 0.2814 (ppp) REVERT: A 1804 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7622 (mtpp) outliers start: 46 outliers final: 34 residues processed: 238 average time/residue: 0.2306 time to fit residues: 82.3112 Evaluate side-chains 228 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 539 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 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS 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 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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 859 ASN A1206 GLN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170104 restraints weight = 15722.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171568 restraints weight = 17092.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172780 restraints weight = 12890.454| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12967 Z= 0.188 Angle : 0.660 9.830 17487 Z= 0.330 Chirality : 0.042 0.198 2015 Planarity : 0.004 0.046 2209 Dihedral : 4.885 35.145 1719 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.05 % Allowed : 21.65 % Favored : 75.29 % 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: -1.28 (0.21), residues: 1582 helix: 0.45 (0.19), residues: 752 sheet: -3.72 (0.52), residues: 56 loop : -1.99 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1549 HIS 0.004 0.001 HIS A1233 PHE 0.026 0.001 PHE A 352 TYR 0.016 0.001 TYR A 572 ARG 0.009 0.001 ARG A 376 =============================================================================== Job complete usr+sys time: 2784.00 seconds wall clock time: 52 minutes 32.84 seconds (3152.84 seconds total)