Starting phenix.real_space_refine
on Thu Feb 13 12:57:24 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1k_33564/02_2025/7y1k_33564.cif"
  }
  resolution = 3.8
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
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=   0.002 sd=   0.068
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      38      5.16       5
     C    5528      2.51       5
     N    1413      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8510
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1164, 8417
          Classifications: {'peptide': 1164}
          Incomplete info: {'truncation_to_alanine': 193}
          Link IDs: {'PTRANS': 34, 'TRANS': 1129}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 762
          Unresolved non-hydrogen angles: 934
          Unresolved non-hydrogen dihedrals: 634
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 8, 'GLU:plan': 33, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 489
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 93
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.08, per 1000 atoms: 0.71
  Number of scatterers: 8510
  At special positions: 0
  Unit cell: (71.724, 100.08, 133.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P       5     15.00
     Mg      2     11.99
     O    1524      8.00
     N    1413      7.00
     C    5528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.56
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      73.5% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 217 through 227
      removed outlier: 3.753A  pdb=" N   ASN A 221 " --> pdb=" O   GLN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 241
      removed outlier: 3.819A  pdb=" N   ASN A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A 233 " --> pdb=" O   TRP A 229 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LEU A 234 " --> pdb=" O   TRP A 230 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   HIS A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG A 240 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
    Processing helix  chain 'A' and resid 284 through 312
      removed outlier: 6.399A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 325
      removed outlier: 3.669A  pdb=" N   LEU A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 394
      removed outlier: 3.700A  pdb=" N   THR A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 416
      removed outlier: 3.547A  pdb=" N   GLY A 408 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLN A 409 " --> pdb=" O   MET A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 427
    Processing helix  chain 'A' and resid 429 through 449
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 4.300A  pdb=" N   VAL A 455 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 497
      removed outlier: 3.516A  pdb=" N   GLU A 487 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 505
      removed outlier: 3.691A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 559
      removed outlier: 3.535A  pdb=" N   SER A 514 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR A 518 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS A 521 " --> pdb=" O   GLU A 517 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   THR A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 543 " --> pdb=" O   MET A 539 " (cutoff:3.500A)
      Proline residue:  A 544  - end of helix
      removed outlier: 3.566A  pdb=" N   VAL A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 607
      removed outlier: 3.682A  pdb=" N   HIS A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   THR A 580 " --> pdb=" O   HIS A 576 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
      removed outlier: 4.454A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   THR A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 607 " --> pdb=" O   ASN A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 4.413A  pdb=" N   LEU A 711 " --> pdb=" O   LYS A 707 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 714 " --> pdb=" O   LEU A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 786 through 793
      removed outlier: 3.521A  pdb=" N   ASP A 791 " --> pdb=" O   GLN A 787 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU A 792 " --> pdb=" O   PRO A 788 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU A 793 " --> pdb=" O   ASP A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 809 through 824
      removed outlier: 3.570A  pdb=" N   ARG A 815 " --> pdb=" O   GLY A 811 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS A 817 " --> pdb=" O   ARG A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 838
      removed outlier: 4.450A  pdb=" N   ALA A 837 " --> pdb=" O   PRO A 834 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 838 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 834 through 838'
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 852 through 859
      removed outlier: 3.502A  pdb=" N   ASP A 857 " --> pdb=" O   LYS A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 872
      removed outlier: 3.684A  pdb=" N   TYR A 871 " --> pdb=" O   LYS A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 912
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 986 through 1016
      removed outlier: 3.679A  pdb=" N   ALA A1012 " --> pdb=" O   ASP A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1075
      removed outlier: 3.940A  pdb=" N   VAL A1053 " --> pdb=" O   THR A1049 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR A1059 " --> pdb=" O   TRP A1055 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A1064 " --> pdb=" O   ALA A1060 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN A1070 " --> pdb=" O   HIS A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.731A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1094
      removed outlier: 3.514A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1091 " --> pdb=" O   LEU A1087 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1102
    Processing helix  chain 'A' and resid 1102 through 1128
    Processing helix  chain 'A' and resid 1130 through 1176
      removed outlier: 3.934A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A1136 " --> pdb=" O   LEU A1132 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      removed outlier: 3.560A  pdb=" N   VAL A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG A1150 " --> pdb=" O   GLN A1146 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL A1151 " --> pdb=" O   LYS A1147 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A1165 " --> pdb=" O   ASP A1161 " (cutoff:3.500A)
      Proline residue:  A1166  - end of helix
    Processing helix  chain 'A' and resid 1177 through 1185
      removed outlier: 3.627A  pdb=" N   ILE A1181 " --> pdb=" O   GLY A1177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1186 through 1237
      removed outlier: 3.694A  pdb=" N   ALA A1204 " --> pdb=" O   THR A1200 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A1222 " --> pdb=" O   ARG A1218 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   CYS A1225 " --> pdb=" O   TYR A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1258
      removed outlier: 3.630A  pdb=" N   LEU A1248 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1285
      removed outlier: 3.621A  pdb=" N   LEU A1265 " --> pdb=" O   VAL A1261 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A1273 " --> pdb=" O   GLU A1269 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL A1275 " --> pdb=" O   GLN A1271 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   GLU A1285 " --> pdb=" O   PHE A1281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1298
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 4.073A  pdb=" N   GLU A1305 " --> pdb=" O   TRP A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1349 through 1357
      removed outlier: 3.723A  pdb=" N   PHE A1356 " --> pdb=" O   SER A1352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
      removed outlier: 3.753A  pdb=" N   LEU A1414 " --> pdb=" O   THR A1410 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP A1415 " --> pdb=" O   ASP A1411 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A1418 " --> pdb=" O   LEU A1414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1423 through 1430
      removed outlier: 3.977A  pdb=" N   SER A1429 " --> pdb=" O   ASN A1425 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A1430 " --> pdb=" O   MET A1426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1439 through 1443
      removed outlier: 3.821A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1461
      removed outlier: 3.587A  pdb=" N   LEU A1452 " --> pdb=" O   GLY A1448 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   CYS A1454 " --> pdb=" O   ARG A1450 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A1455 " --> pdb=" O   GLN A1451 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A1460 " --> pdb=" O   ALA A1456 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG A1461 " --> pdb=" O   ARG A1457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1491
      removed outlier: 3.826A  pdb=" N   ILE A1482 " --> pdb=" O   ALA A1478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1502 through 1507
    Processing helix  chain 'A' and resid 1525 through 1533
      removed outlier: 3.526A  pdb=" N   LEU A1530 " --> pdb=" O   GLY A1526 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS A1533 " --> pdb=" O   LEU A1529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1535 through 1542
    Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 691
      removed outlier: 5.353A  pdb=" N   SER A 685 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   PHE A 675 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE A 689 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   THR A 671 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ILE A 691 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   LYS A 669 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR A 671 " --> pdb=" O   LYS A 724 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 724 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   GLY A 673 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLU A 722 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR A 720 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 830 through 832
      removed outlier: 7.272A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   THR A 697 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   THR A 866 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   ILE A 699 " --> pdb=" O   THR A 866 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ILE A 878 " --> pdb=" O   GLU A 889 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   GLU A 889 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA A 880 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1328
      removed outlier: 5.168A  pdb=" N   LEU A1313 " --> pdb=" O   HIS A1327 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1339 through 1342
      removed outlier: 6.460A  pdb=" N   GLY A1339 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   PHE A1515 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   CYS A1341 " --> pdb=" O   PHE A1515 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   SER A1516 " --> pdb=" O   LEU A1520 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   LEU A1520 " --> pdb=" O   SER A1516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1388
      removed outlier: 6.755A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398

    586 hydrogen bonds defined for protein.
    1710 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: 3.07

  Time building geometry restraints manager: 2.90 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 1317
        1.31 -     1.43: 2306
        1.43 -     1.56: 4988
        1.56 -     1.69: 8
        1.69 -     1.81: 59
  Bond restraints: 8678
  Sorted by residual:
  bond pdb=" C16 BJX A1604 "
       pdb=" N1  BJX A1604 "
    ideal  model  delta    sigma   weight residual
    1.344  1.452 -0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" C21 BJX A1604 "
       pdb=" O1  BJX A1604 "
    ideal  model  delta    sigma   weight residual
    1.347  1.401 -0.054 2.00e-02 2.50e+03 7.16e+00
  bond pdb=" N   SER A1349 "
       pdb=" CA  SER A1349 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.28e-02 6.10e+03 4.29e+00
  bond pdb=" N   ALA A 558 "
       pdb=" CA  ALA A 558 "
    ideal  model  delta    sigma   weight residual
    1.459  1.434  0.025 1.28e-02 6.10e+03 3.73e+00
  bond pdb=" CA  ALA A 558 "
       pdb=" C   ALA A 558 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.025 1.35e-02 5.49e+03 3.56e+00
  ... (remaining 8673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 11701
        1.95 -     3.89: 136
        3.89 -     5.84: 37
        5.84 -     7.79: 8
        7.79 -     9.73: 2
  Bond angle restraints: 11884
  Sorted by residual:
  angle pdb=" N   MET A1284 "
        pdb=" CA  MET A1284 "
        pdb=" C   MET A1284 "
      ideal   model   delta    sigma   weight residual
     111.07  120.80   -9.73 1.07e+00 8.73e-01 8.28e+01
  angle pdb=" N   LYS A1348 "
        pdb=" CA  LYS A1348 "
        pdb=" C   LYS A1348 "
      ideal   model   delta    sigma   weight residual
     111.14  119.97   -8.83 1.08e+00 8.57e-01 6.69e+01
  angle pdb=" N   GLU A1285 "
        pdb=" CA  GLU A1285 "
        pdb=" C   GLU A1285 "
      ideal   model   delta    sigma   weight residual
     108.42  116.14   -7.72 1.54e+00 4.22e-01 2.51e+01
  angle pdb=" N   SER A1346 "
        pdb=" CA  SER A1346 "
        pdb=" C   SER A1346 "
      ideal   model   delta    sigma   weight residual
     110.80  118.15   -7.35 2.13e+00 2.20e-01 1.19e+01
  angle pdb=" N   SER A 559 "
        pdb=" CA  SER A 559 "
        pdb=" C   SER A 559 "
      ideal   model   delta    sigma   weight residual
     109.07  114.53   -5.46 1.61e+00 3.86e-01 1.15e+01
  ... (remaining 11879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.47: 4981
       31.47 -    62.94: 95
       62.94 -    94.41: 5
       94.41 -   125.88: 2
      125.88 -   157.35: 2
  Dihedral angle restraints: 5085
    sinusoidal: 1703
      harmonic: 3382
  Sorted by residual:
  dihedral pdb=" O1B ADP A1605 "
           pdb=" O3A ADP A1605 "
           pdb=" PB  ADP A1605 "
           pdb=" PA  ADP A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -169.59  109.59     1      2.00e+01 2.50e-03 3.20e+01
  dihedral pdb=" O2A ADP A1605 "
           pdb=" O3A ADP A1605 "
           pdb=" PA  ADP A1605 "
           pdb=" PB  ADP A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   43.72 -103.72     1      2.00e+01 2.50e-03 2.97e+01
  dihedral pdb=" O   BJX A1604 "
           pdb=" C16 BJX A1604 "
           pdb=" C17 BJX A1604 "
           pdb=" C18 BJX A1604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      10.31  167.66 -157.35     1      3.00e+01 1.11e-03 2.05e+01
  ... (remaining 5082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1222
       0.050 -    0.099: 214
       0.099 -    0.149: 46
       0.149 -    0.198: 0
       0.198 -    0.248: 3
  Chirality restraints: 1485
  Sorted by residual:
  chirality pdb=" CA  LYS A1348 "
            pdb=" N   LYS A1348 "
            pdb=" C   LYS A1348 "
            pdb=" CB  LYS A1348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  MET A1284 "
            pdb=" N   MET A1284 "
            pdb=" C   MET A1284 "
            pdb=" CB  MET A1284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  SER A1346 "
            pdb=" N   SER A1346 "
            pdb=" C   SER A1346 "
            pdb=" CB  SER A1346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1482 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1104 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A1105 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A1105 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1105 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1345 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   GLY A1345 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLY A1345 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER A1346 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1103 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO A1104 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A1104 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1104 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 63
        2.59 -     3.17: 7921
        3.17 -     3.74: 13526
        3.74 -     4.32: 17781
        4.32 -     4.90: 29180
  Nonbonded interactions: 68471
  Sorted by model distance:
  nonbonded pdb="MG    MG A1603 "
            pdb=" O2B ADP A1605 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" O2B ATP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" O1G ATP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O3B ATP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.121 2.170
  nonbonded pdb="MG    MG A1603 "
            pdb=" O1B ADP A1605 "
     model   vdw
     2.159 2.170
  ... (remaining 68466 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.930
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
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   0.108   8678  Z= 0.282
  Angle     :  0.606   9.734  11884  Z= 0.318
  Chirality :  0.041   0.248   1485
  Planarity :  0.004   0.046   1452
  Dihedral  : 12.888 157.353   2893
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  :  7.39 %
    Favored  : 89.66 %
  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:  0.96 (0.25), residues: 1150
  helix:  0.93 (0.19), residues: 745
  sheet: -1.05 (0.84), residues: 37
  loop :  0.49 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 507 
 HIS   0.004   0.001   HIS A 555 
 PHE   0.008   0.001   PHE A 569 
 TYR   0.011   0.001   TYR A 290 
 ARG   0.002   0.000   ARG A1461 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  239 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (m90)
REVERT: A  356 PHE cc_start: 0.8518 (t80) cc_final: 0.8278 (t80)
REVERT: A  479 LYS cc_start: 0.9225 (tttt) cc_final: 0.8695 (ttmm)
REVERT: A  571 SER cc_start: 0.8710 (m) cc_final: 0.8499 (t)
REVERT: A  698 MET cc_start: 0.3873 (mtp) cc_final: 0.3274 (ttm)
REVERT: A  823 TYR cc_start: 0.6147 (t80) cc_final: 0.5500 (t80)
REVERT: A 1050 SER cc_start: 0.9380 (m) cc_final: 0.9167 (p)
REVERT: A 1089 LEU cc_start: 0.9183 (tp) cc_final: 0.8953 (tt)
REVERT: A 1228 LEU cc_start: 0.9136 (tp) cc_final: 0.8879 (tt)
REVERT: A 1271 GLN cc_start: 0.8715 (mt0) cc_final: 0.8465 (mt0)
REVERT: A 1317 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.3633 (p90)
REVERT: A 1373 ILE cc_start: 0.8880 (pt) cc_final: 0.8472 (pt)
  outliers start: 24
  outliers final: 5
  residues processed: 195
  average time/residue: 0.1753
  time to fit residues: 49.8006
Evaluate side-chains
  123 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue 1186 HIS
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1317 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.130158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.104484 restraints weight = 17536.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.107274 restraints weight = 8187.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.108967 restraints weight = 4778.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8678  Z= 0.216
  Angle     :  0.597   7.502  11884  Z= 0.308
  Chirality :  0.041   0.185   1485
  Planarity :  0.004   0.054   1452
  Dihedral  : 10.561 149.955   1300
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.32 %
    Favored  : 84.24 %
  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:  1.62 (0.25), residues: 1150
  helix:  1.66 (0.18), residues: 775
  sheet: -1.20 (0.87), residues: 39
  loop :  0.13 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 507 
 HIS   0.005   0.001   HIS A 555 
 PHE   0.017   0.001   PHE A1184 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.007   0.001   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  239 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8401 (m90)
REVERT: A  255 MET cc_start: 0.8239 (mtp) cc_final: 0.7735 (ttm)
REVERT: A  823 TYR cc_start: 0.6170 (t80) cc_final: 0.5622 (t80)
REVERT: A  993 MET cc_start: 0.8838 (tmm) cc_final: 0.8272 (tmm)
REVERT: A  997 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8628 (ttmt)
REVERT: A 1050 SER cc_start: 0.9444 (m) cc_final: 0.9207 (p)
REVERT: A 1071 LYS cc_start: 0.8423 (tptt) cc_final: 0.8194 (tptt)
REVERT: A 1259 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8345 (t0)
REVERT: A 1271 GLN cc_start: 0.8461 (mt0) cc_final: 0.7897 (mp10)
REVERT: A 1373 ILE cc_start: 0.8507 (pt) cc_final: 0.8202 (pt)
  outliers start: 28
  outliers final: 18
  residues processed: 163
  average time/residue: 0.1587
  time to fit residues: 38.8147
Evaluate side-chains
  123 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  428 CYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1460 VAL
Chi-restraints excluded: chain A residue 1529 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 102 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.132205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.106527 restraints weight = 17929.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109341 restraints weight = 8320.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.111115 restraints weight = 4824.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8678  Z= 0.170
  Angle     :  0.549   8.519  11884  Z= 0.272
  Chirality :  0.040   0.211   1485
  Planarity :  0.004   0.056   1452
  Dihedral  :  9.348 153.045   1296
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.16 %
    Favored  : 82.51 %
  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:  2.10 (0.25), residues: 1150
  helix:  2.02 (0.18), residues: 775
  sheet: -1.07 (0.91), residues: 39
  loop :  0.34 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.015   0.001   PHE A1149 
 TYR   0.010   0.001   TYR A 290 
 ARG   0.004   0.000   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8410 (m90)
REVERT: A  504 LEU cc_start: 0.8139 (mt) cc_final: 0.7876 (mt)
REVERT: A  718 MET cc_start: 0.7492 (ptm) cc_final: 0.7135 (ptm)
REVERT: A  823 TYR cc_start: 0.6068 (t80) cc_final: 0.5598 (t80)
REVERT: A  993 MET cc_start: 0.8850 (tmm) cc_final: 0.8120 (tmm)
REVERT: A  997 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8484 (ttmt)
REVERT: A 1050 SER cc_start: 0.9456 (m) cc_final: 0.9146 (p)
REVERT: A 1259 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8257 (t0)
REVERT: A 1271 GLN cc_start: 0.8312 (mt0) cc_final: 0.7765 (mp10)
REVERT: A 1317 TYR cc_start: 0.4484 (OUTLIER) cc_final: 0.3467 (p90)
REVERT: A 1373 ILE cc_start: 0.8236 (pt) cc_final: 0.7964 (pt)
  outliers start: 27
  outliers final: 17
  residues processed: 163
  average time/residue: 0.1501
  time to fit residues: 37.3314
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  428 CYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1529 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 59 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 112 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 55 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9990
   chunk 99 optimal weight:    8.9990
   overall best weight:    0.6520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.128220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.101661 restraints weight = 18061.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.104410 restraints weight = 8619.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.106116 restraints weight = 5061.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8678  Z= 0.159
  Angle     :  0.571   8.451  11884  Z= 0.274
  Chirality :  0.041   0.283   1485
  Planarity :  0.004   0.058   1452
  Dihedral  :  8.872 147.280   1293
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.89 %
    Favored  : 80.42 %
  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:  2.18 (0.25), residues: 1150
  helix:  2.10 (0.18), residues: 784
  sheet: -0.40 (0.80), residues: 50
  loop :  0.18 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.012   0.001   PHE A 569 
 TYR   0.010   0.001   TYR A1257 
 ARG   0.003   0.000   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  219 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7753 (t80)
REVERT: A  231 MET cc_start: 0.8525 (mmm) cc_final: 0.7934 (tpt)
REVERT: A  239 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8436 (m90)
REVERT: A  487 GLU cc_start: 0.7714 (tp30) cc_final: 0.7282 (tp30)
REVERT: A  504 LEU cc_start: 0.8083 (mt) cc_final: 0.7880 (mt)
REVERT: A  698 MET cc_start: 0.3575 (mtp) cc_final: 0.3002 (ttm)
REVERT: A  718 MET cc_start: 0.7637 (ptm) cc_final: 0.7339 (ptm)
REVERT: A  823 TYR cc_start: 0.6148 (t80) cc_final: 0.5635 (t80)
REVERT: A  993 MET cc_start: 0.8853 (tmm) cc_final: 0.8395 (tmm)
REVERT: A 1259 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8253 (t0)
REVERT: A 1271 GLN cc_start: 0.8312 (mt0) cc_final: 0.7773 (mp10)
REVERT: A 1418 LEU cc_start: 0.6419 (tp) cc_final: 0.6204 (tp)
  outliers start: 30
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1422
  time to fit residues: 33.8306
Evaluate side-chains
  141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1460 VAL
Chi-restraints excluded: chain A residue 1529 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   chunk 41 optimal weight:    0.3980
   chunk 106 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 64 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.127442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.100980 restraints weight = 17850.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.103635 restraints weight = 8627.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.105369 restraints weight = 5138.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8678  Z= 0.188
  Angle     :  0.553   7.977  11884  Z= 0.267
  Chirality :  0.040   0.228   1485
  Planarity :  0.004   0.057   1452
  Dihedral  :  8.551 145.042   1291
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.86 %
    Favored  : 78.45 %
  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:  2.24 (0.25), residues: 1150
  helix:  2.17 (0.18), residues: 785
  sheet: -0.47 (0.80), residues: 50
  loop :  0.15 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.015   0.001   PHE A 569 
 TYR   0.013   0.001   TYR A 228 
 ARG   0.003   0.000   ARG A1382 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  219 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (t80)
REVERT: A  239 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8482 (m90)
REVERT: A  487 GLU cc_start: 0.7979 (tp30) cc_final: 0.7604 (tp30)
REVERT: A  823 TYR cc_start: 0.6081 (t80) cc_final: 0.5594 (t80)
REVERT: A  993 MET cc_start: 0.8901 (tmm) cc_final: 0.8318 (tmm)
REVERT: A 1056 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7729 (tmm)
REVERT: A 1259 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8327 (t0)
REVERT: A 1271 GLN cc_start: 0.8322 (mt0) cc_final: 0.7798 (mp10)
  outliers start: 30
  outliers final: 21
  residues processed: 139
  average time/residue: 0.1491
  time to fit residues: 32.1899
Evaluate side-chains
  139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1460 VAL
Chi-restraints excluded: chain A residue 1529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.127942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.101251 restraints weight = 17753.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.103899 restraints weight = 8610.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.105609 restraints weight = 5138.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8678  Z= 0.171
  Angle     :  0.551   8.049  11884  Z= 0.264
  Chirality :  0.040   0.257   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  8.351 143.348   1291
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.35 %
    Favored  : 77.71 %
  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:  2.41 (0.25), residues: 1150
  helix:  2.29 (0.18), residues: 776
  sheet: -0.41 (0.81), residues: 50
  loop :  0.28 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.015   0.001   PHE A 569 
 TYR   0.020   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7770 (t80)
REVERT: A  239 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8427 (m90)
REVERT: A  823 TYR cc_start: 0.6143 (t80) cc_final: 0.5769 (t80)
REVERT: A  892 LEU cc_start: -0.0203 (OUTLIER) cc_final: -0.0613 (tm)
REVERT: A  993 MET cc_start: 0.8899 (tmm) cc_final: 0.8172 (tmm)
REVERT: A 1056 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7741 (tmm)
REVERT: A 1071 LYS cc_start: 0.8236 (tptt) cc_final: 0.7924 (tptt)
REVERT: A 1259 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8333 (t0)
REVERT: A 1271 GLN cc_start: 0.8294 (mt0) cc_final: 0.8044 (mt0)
REVERT: A 1422 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6842 (tm-30)
  outliers start: 32
  outliers final: 20
  residues processed: 144
  average time/residue: 0.1434
  time to fit residues: 32.2974
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1460 VAL
Chi-restraints excluded: chain A residue 1529 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 112 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 108 optimal weight:    0.4980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.128264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.101599 restraints weight = 17919.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.104311 restraints weight = 8685.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106027 restraints weight = 5141.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8678  Z= 0.164
  Angle     :  0.551   8.188  11884  Z= 0.262
  Chirality :  0.040   0.271   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  8.133 141.200   1289
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.09 %
    Favored  : 77.09 %
  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:  2.44 (0.25), residues: 1150
  helix:  2.32 (0.18), residues: 780
  sheet: -0.28 (0.82), residues: 50
  loop :  0.23 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.000   HIS A1001 
 PHE   0.017   0.001   PHE A1356 
 TYR   0.018   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1357 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7786 (t80)
REVERT: A  239 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8425 (m90)
REVERT: A  718 MET cc_start: 0.7359 (ptm) cc_final: 0.7062 (ptm)
REVERT: A  823 TYR cc_start: 0.6064 (t80) cc_final: 0.5753 (t80)
REVERT: A  892 LEU cc_start: -0.0177 (OUTLIER) cc_final: -0.0591 (tm)
REVERT: A  993 MET cc_start: 0.8918 (tmm) cc_final: 0.8332 (tmm)
REVERT: A 1056 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7672 (tmm)
REVERT: A 1259 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8339 (t0)
REVERT: A 1271 GLN cc_start: 0.8272 (mt0) cc_final: 0.7995 (mt0)
REVERT: A 1418 LEU cc_start: 0.6603 (tp) cc_final: 0.6338 (tp)
  outliers start: 31
  outliers final: 21
  residues processed: 143
  average time/residue: 0.1407
  time to fit residues: 31.5742
Evaluate side-chains
  140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1002 SER
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.129185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102320 restraints weight = 17885.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.105036 restraints weight = 8671.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.106741 restraints weight = 5140.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8678  Z= 0.154
  Angle     :  0.556   8.686  11884  Z= 0.262
  Chirality :  0.040   0.323   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  7.929 139.035   1289
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.95 %
    Favored  : 76.48 %
  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:  2.54 (0.25), residues: 1150
  helix:  2.36 (0.18), residues: 782
  sheet: -0.14 (0.84), residues: 50
  loop :  0.37 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.019   0.001   PHE A 675 
 TYR   0.016   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7757 (t80)
REVERT: A  239 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8442 (m90)
REVERT: A  823 TYR cc_start: 0.6045 (t80) cc_final: 0.5685 (t80)
REVERT: A  892 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.0608 (tm)
REVERT: A  993 MET cc_start: 0.8829 (tmm) cc_final: 0.8367 (tmm)
REVERT: A 1056 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7668 (tmm)
REVERT: A 1071 LYS cc_start: 0.8371 (tptt) cc_final: 0.8037 (tptt)
REVERT: A 1259 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8347 (t0)
REVERT: A 1271 GLN cc_start: 0.8233 (mt0) cc_final: 0.7966 (mt0)
REVERT: A 1352 SER cc_start: 0.9494 (t) cc_final: 0.9249 (p)
REVERT: A 1422 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6741 (tm-30)
  outliers start: 29
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1579
  time to fit residues: 37.0590
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1002 SER
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1146 GLN
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 ASN
A 540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.128789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.101633 restraints weight = 18110.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.104341 restraints weight = 8842.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106077 restraints weight = 5287.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8678  Z= 0.175
  Angle     :  0.573   9.924  11884  Z= 0.270
  Chirality :  0.040   0.294   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  7.812 137.600   1289
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.57 %
    Favored  : 75.86 %
  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:  2.53 (0.25), residues: 1150
  helix:  2.37 (0.18), residues: 782
  sheet: -0.11 (0.83), residues: 50
  loop :  0.29 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 677 
 HIS   0.002   0.000   HIS A1001 
 PHE   0.015   0.001   PHE A 569 
 TYR   0.015   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1218 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7760 (t80)
REVERT: A  239 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8422 (m90)
REVERT: A  390 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8239 (t0)
REVERT: A  675 PHE cc_start: 0.7935 (m-80) cc_final: 0.7721 (m-80)
REVERT: A  823 TYR cc_start: 0.5980 (t80) cc_final: 0.5482 (t80)
REVERT: A  892 LEU cc_start: -0.0161 (OUTLIER) cc_final: -0.0570 (tm)
REVERT: A  993 MET cc_start: 0.8851 (tmm) cc_final: 0.8361 (tmm)
REVERT: A 1050 SER cc_start: 0.9480 (m) cc_final: 0.9236 (p)
REVERT: A 1056 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7654 (tmm)
REVERT: A 1071 LYS cc_start: 0.8303 (tptt) cc_final: 0.7948 (tptt)
REVERT: A 1259 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8382 (t0)
REVERT: A 1271 GLN cc_start: 0.8242 (mt0) cc_final: 0.7972 (mt0)
REVERT: A 1352 SER cc_start: 0.9489 (t) cc_final: 0.9247 (p)
REVERT: A 1422 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6778 (tm-30)
  outliers start: 29
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1494
  time to fit residues: 32.6954
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1002 SER
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1263 ARG
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 91 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.129610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.102501 restraints weight = 17823.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105228 restraints weight = 8759.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.106863 restraints weight = 5218.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8678  Z= 0.150
  Angle     :  0.578  12.587  11884  Z= 0.268
  Chirality :  0.040   0.332   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  7.717 136.324   1289
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.69 %
    Favored  : 76.11 %
  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:  2.59 (0.25), residues: 1150
  helix:  2.45 (0.18), residues: 776
  sheet: -0.12 (0.83), residues: 50
  loop :  0.27 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 677 
 HIS   0.003   0.000   HIS A1001 
 PHE   0.013   0.001   PHE A 569 
 TYR   0.014   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1218 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7762 (t80)
REVERT: A  239 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8409 (m90)
REVERT: A  390 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8285 (t0)
REVERT: A  823 TYR cc_start: 0.5943 (t80) cc_final: 0.5489 (t80)
REVERT: A  892 LEU cc_start: -0.0216 (OUTLIER) cc_final: -0.0614 (tm)
REVERT: A  993 MET cc_start: 0.8878 (tmm) cc_final: 0.8383 (tmm)
REVERT: A 1050 SER cc_start: 0.9489 (m) cc_final: 0.9257 (p)
REVERT: A 1056 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7636 (tmm)
REVERT: A 1071 LYS cc_start: 0.8292 (tptt) cc_final: 0.7933 (tptt)
REVERT: A 1259 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8387 (t0)
REVERT: A 1271 GLN cc_start: 0.8257 (mt0) cc_final: 0.7990 (mt0)
REVERT: A 1352 SER cc_start: 0.9493 (t) cc_final: 0.9251 (p)
REVERT: A 1422 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6768 (tm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 145
  average time/residue: 0.1505
  time to fit residues: 33.7209
Evaluate side-chains
  144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1002 SER
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1263 ARG
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   chunk 99 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.128250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.101140 restraints weight = 18130.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.103813 restraints weight = 8933.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.105547 restraints weight = 5350.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8678  Z= 0.196
  Angle     :  0.588  11.780  11884  Z= 0.276
  Chirality :  0.041   0.293   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  7.680 135.830   1289
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.69 %
    Favored  : 75.74 %
  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:  2.58 (0.25), residues: 1150
  helix:  2.44 (0.18), residues: 770
  sheet: -0.10 (0.84), residues: 50
  loop :  0.29 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.015   0.001   PHE A 569 
 TYR   0.013   0.001   TYR A 228 
 ARG   0.002   0.000   ARG A1382 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2466.77 seconds
wall clock time: 45 minutes 9.71 seconds (2709.71 seconds total)