Starting phenix.real_space_refine
on Thu Jul  2 14:28:35 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1k_33564/07_2026/7y1k_33564.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ARG:plan': 16, 'ASP:plan': 26, 'GLU:plan': 33, 'PHE:plan': 8, 'ASN:plan1': 9, 'GLN:plan1': 16, 'TYR:plan': 3, 'HIS:plan': 6, 'TRP:plan': 1}
          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: 1.39, per 1000 atoms: 0.16
  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: 0.62
  Conformation dependent library (CDL) restraints added in 205.1 milliseconds
  

  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: 0.27
  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: 0.98

  Time building geometry restraints manager: 0.81 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: 4961
       31.47 -    62.94: 77
       62.94 -    94.41: 2
       94.41 -   125.88: 2
      125.88 -   157.35: 2
  Dihedral angle restraints: 5044
    sinusoidal: 1662
      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 5041 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:             2.040
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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= 0.211
  Angle     :  0.606   9.734  11884  Z= 0.318
  Chirality :  0.041   0.248   1485
  Planarity :  0.004   0.046   1452
  Dihedral  : 12.265 157.353   2852
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG A1461 
 TYR   0.011   0.001   TYR A 290 
 PHE   0.008   0.001   PHE A 569 
 TRP   0.015   0.001   TRP A 507 
 HIS   0.004   0.001   HIS A 555 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.21 ( 8678)
  covalent geometry    : angle       0.60580 /  0.32 (11884)
  hydrogen bonds       : bond        0.26087 / 17.58 (  586)
  hydrogen bonds       : angle       8.02158 /  5.93 ( 1710)

*********************** 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  : 0.243 
Fit side-chains
REVERT: A  239 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8247 (m90)
REVERT: A  356 PHE cc_start: 0.8518 (t80) cc_final: 0.8282 (t80)
REVERT: A  479 LYS cc_start: 0.9225 (tttt) cc_final: 0.8694 (ttmm)
REVERT: A  571 SER cc_start: 0.8710 (m) cc_final: 0.8495 (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: 0.9381 (m) cc_final: 0.9166 (p)
REVERT: A 1089 LEU cc_start: 0.9183 (tp) cc_final: 0.8952 (tt)
REVERT: A 1228 LEU cc_start: 0.9136 (tp) cc_final: 0.8874 (tt)
REVERT: A 1271 GLN cc_start: 0.8716 (mt0) cc_final: 0.8466 (mt0)
REVERT: A 1317 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.3635 (p90)
REVERT: A 1373 ILE cc_start: 0.8880 (pt) cc_final: 0.8475 (pt)
  outliers start: 24
  outliers final: 5
  residues processed: 195
  average time/residue: 0.0612
  time to fit residues: 17.7915
Evaluate side-chains
  121 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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 108 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3839 r_free = 0.3839 target = 0.130777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.105161 restraints weight = 17669.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.107975 restraints weight = 8264.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.109602 restraints weight = 4802.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.110667 restraints weight = 3372.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111150 restraints weight = 2703.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8678  Z= 0.155
  Angle     :  0.603   9.824  11884  Z= 0.303
  Chirality :  0.042   0.207   1485
  Planarity :  0.004   0.054   1452
  Dihedral  :  9.182 152.082   1259
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 11.21 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.25), residues: 1150
  helix:  1.60 (0.18), residues: 776
  sheet: -1.14 (0.89), residues: 39
  loop :  0.10 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1091 
 TYR   0.018   0.001   TYR A1009 
 PHE   0.018   0.001   PHE A1184 
 TRP   0.017   0.002   TRP A 507 
 HIS   0.004   0.001   HIS A 555 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.16 ( 8678)
  covalent geometry    : angle       0.60269 /  0.30 (11884)
  hydrogen bonds       : bond        0.05364 /  3.60 (  586)
  hydrogen bonds       : angle       4.84880 /  3.56 ( 1710)

*********************** 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
  181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  239 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8408 (m90)
REVERT: A  255 MET cc_start: 0.8116 (mtp) cc_final: 0.7642 (ttm)
REVERT: A  387 MET cc_start: 0.8440 (tpp) cc_final: 0.7928 (ttm)
REVERT: A  407 LEU cc_start: 0.8854 (tt) cc_final: 0.8599 (tt)
REVERT: A  823 TYR cc_start: 0.6228 (t80) cc_final: 0.5678 (t80)
REVERT: A  993 MET cc_start: 0.8824 (tmm) cc_final: 0.8281 (tmm)
REVERT: A  997 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8629 (ttmt)
REVERT: A 1050 SER cc_start: 0.9437 (m) cc_final: 0.9217 (p)
REVERT: A 1259 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8304 (t0)
REVERT: A 1271 GLN cc_start: 0.8451 (mt0) cc_final: 0.7884 (mp10)
REVERT: A 1373 ILE cc_start: 0.8449 (pt) cc_final: 0.8174 (pt)
REVERT: A 1427 VAL cc_start: 0.8613 (t) cc_final: 0.8166 (t)
  outliers start: 30
  outliers final: 18
  residues processed: 173
  average time/residue: 0.0574
  time to fit residues: 14.9230
Evaluate side-chains
  125 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  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 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 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 105 optimal weight:    0.0470
   chunk 114 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0040
   chunk 35 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.4890

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3792 r_free = 0.3792 target = 0.128288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.101942 restraints weight = 17795.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.104704 restraints weight = 8487.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.106458 restraints weight = 4952.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.107508 restraints weight = 3419.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.107997 restraints weight = 2724.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8678  Z= 0.118
  Angle     :  0.550   9.630  11884  Z= 0.270
  Chirality :  0.039   0.210   1485
  Planarity :  0.004   0.056   1452
  Dihedral  :  8.372 159.092   1255
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.02 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.25), residues: 1150
  helix:  2.01 (0.18), residues: 780
  sheet: -1.00 (0.92), residues: 39
  loop :  0.24 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1218 
 TYR   0.009   0.001   TYR A 290 
 PHE   0.017   0.001   PHE A 583 
 TRP   0.007   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.12 ( 8678)
  covalent geometry    : angle       0.55006 /  0.27 (11884)
  hydrogen bonds       : bond        0.04457 /  2.96 (  586)
  hydrogen bonds       : angle       4.28205 /  3.16 ( 1710)

*********************** 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
  167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  231 MET cc_start: 0.8557 (mmm) cc_final: 0.7981 (tpt)
REVERT: A  239 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8451 (m90)
REVERT: A  504 LEU cc_start: 0.8133 (mt) cc_final: 0.7920 (mt)
REVERT: A  675 PHE cc_start: 0.8175 (m-80) cc_final: 0.7920 (m-80)
REVERT: A  823 TYR cc_start: 0.6081 (t80) cc_final: 0.5618 (t80)
REVERT: A  993 MET cc_start: 0.8852 (tmm) cc_final: 0.8174 (tmm)
REVERT: A  997 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8488 (ttmt)
REVERT: A 1050 SER cc_start: 0.9457 (m) cc_final: 0.9250 (p)
REVERT: A 1195 LEU cc_start: 0.8620 (mt) cc_final: 0.8412 (mp)
REVERT: A 1259 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8293 (t0)
REVERT: A 1271 GLN cc_start: 0.8328 (mt0) cc_final: 0.7773 (mp10)
REVERT: A 1317 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.3418 (p90)
REVERT: A 1373 ILE cc_start: 0.8246 (pt) cc_final: 0.7970 (pt)
  outliers start: 25
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0497
  time to fit residues: 12.7665
Evaluate side-chains
  137 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  444 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  474 LEU
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 1219 THR
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 39 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 110 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0980
   chunk 45 optimal weight:    6.9990
   chunk 112 optimal weight:    4.9990
   overall best weight:    2.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3736 r_free = 0.3736 target = 0.124082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.097673 restraints weight = 18426.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100269 restraints weight = 8991.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.101937 restraints weight = 5354.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.102948 restraints weight = 3737.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103465 restraints weight = 2973.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8678  Z= 0.211
  Angle     :  0.644  10.922  11884  Z= 0.317
  Chirality :  0.043   0.213   1485
  Planarity :  0.004   0.059   1452
  Dihedral  :  8.298 154.720   1250
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 17.36 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.25), residues: 1150
  helix:  1.77 (0.18), residues: 789
  sheet: -1.11 (0.92), residues: 39
  loop : -0.12 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1382 
 TYR   0.016   0.002   TYR A1317 
 PHE   0.018   0.002   PHE A 583 
 TRP   0.010   0.001   TRP A1260 
 HIS   0.004   0.001   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.21 ( 8678)
  covalent geometry    : angle       0.64435 /  0.32 (11884)
  hydrogen bonds       : bond        0.04593 /  3.07 (  586)
  hydrogen bonds       : angle       4.39254 /  3.24 ( 1710)

*********************** 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
  154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7761 (t80)
REVERT: A  239 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8518 (m90)
REVERT: A  387 MET cc_start: 0.8601 (tpp) cc_final: 0.8045 (ttm)
REVERT: A  390 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8429 (t0)
REVERT: A  487 GLU cc_start: 0.7819 (tp30) cc_final: 0.7462 (tp30)
REVERT: A  823 TYR cc_start: 0.6093 (t80) cc_final: 0.5611 (t80)
REVERT: A  993 MET cc_start: 0.8875 (tmm) cc_final: 0.8389 (tmm)
REVERT: A 1259 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8432 (t0)
REVERT: A 1317 TYR cc_start: 0.4428 (OUTLIER) cc_final: 0.4140 (p90)
REVERT: A 1373 ILE cc_start: 0.8384 (pt) cc_final: 0.8156 (pt)
REVERT: A 1439 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6907 (p)
  outliers start: 38
  outliers final: 26
  residues processed: 144
  average time/residue: 0.0587
  time to fit residues: 13.3957
Evaluate side-chains
  140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  318 ILE
Chi-restraints excluded: chain A residue  390 ASN
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  472 THR
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  492 THR
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  829 VAL
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 1146 GLN
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1219 THR
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 1439 THR
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 37 optimal weight:    0.0980
   chunk 87 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 115 optimal weight:    0.3980
   chunk 55 optimal weight:    0.7980
   chunk 88 optimal weight:    0.4980
   chunk 47 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3804 r_free = 0.3804 target = 0.129006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.102396 restraints weight = 17978.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.105201 restraints weight = 8632.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.106976 restraints weight = 5068.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.107946 restraints weight = 3514.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.108582 restraints weight = 2817.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8678  Z= 0.113
  Angle     :  0.559  11.159  11884  Z= 0.268
  Chirality :  0.040   0.264   1485
  Planarity :  0.004   0.058   1452
  Dihedral  :  8.116 155.377   1250
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.21 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.25), residues: 1150
  helix:  2.09 (0.19), residues: 787
  sheet: -0.53 (0.80), residues: 50
  loop :  0.07 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1457 
 TYR   0.013   0.001   TYR A 228 
 PHE   0.024   0.001   PHE A 583 
 TRP   0.010   0.001   TRP A 677 
 HIS   0.003   0.001   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 ( 8678)
  covalent geometry    : angle       0.55911 /  0.27 (11884)
  hydrogen bonds       : bond        0.03921 /  2.61 (  586)
  hydrogen bonds       : angle       3.97955 /  2.95 ( 1710)

*********************** 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
  160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  219 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7745 (t80)
REVERT: A  239 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8384 (m90)
REVERT: A  375 GLU cc_start: 0.7642 (tt0) cc_final: 0.7377 (mt-10)
REVERT: A  487 GLU cc_start: 0.7966 (tp30) cc_final: 0.7592 (tp30)
REVERT: A  823 TYR cc_start: 0.6026 (t80) cc_final: 0.5726 (t80)
REVERT: A  892 LEU cc_start: -0.0145 (OUTLIER) cc_final: -0.0563 (tm)
REVERT: A  993 MET cc_start: 0.8874 (tmm) cc_final: 0.8390 (tmm)
REVERT: A 1259 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8365 (t0)
REVERT: A 1352 SER cc_start: 0.9493 (t) cc_final: 0.9249 (p)
REVERT: A 1439 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6948 (p)
  outliers start: 27
  outliers final: 15
  residues processed: 153
  average time/residue: 0.0624
  time to fit residues: 15.2108
Evaluate side-chains
  139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
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  460 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  577 ILE
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  892 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
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 1439 THR
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 82 optimal weight:    0.5980
   chunk 80 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0980
   chunk 44 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3801 r_free = 0.3801 target = 0.128701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.101985 restraints weight = 17824.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.104696 restraints weight = 8690.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.106485 restraints weight = 5171.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.107409 restraints weight = 3577.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.108130 restraints weight = 2886.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3578

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= 0.117
  Angle     :  0.571  12.300  11884  Z= 0.269
  Chirality :  0.041   0.324   1485
  Planarity :  0.004   0.057   1452
  Dihedral  :  8.064 153.381   1250
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.25), residues: 1150
  helix:  2.21 (0.18), residues: 783
  sheet: -0.46 (0.81), residues: 50
  loop :  0.31 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1218 
 TYR   0.019   0.001   TYR A 228 
 PHE   0.025   0.001   PHE A 583 
 TRP   0.008   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 8678)
  covalent geometry    : angle       0.57095 /  0.27 (11884)
  hydrogen bonds       : bond        0.03840 /  2.54 (  586)
  hydrogen bonds       : angle       3.94258 /  2.92 ( 1710)

*********************** 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
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  219 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7712 (t80)
REVERT: A  231 MET cc_start: 0.8485 (mmm) cc_final: 0.7758 (tpt)
REVERT: A  239 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8383 (m90)
REVERT: A  823 TYR cc_start: 0.5981 (t80) cc_final: 0.5722 (t80)
REVERT: A  892 LEU cc_start: -0.0065 (OUTLIER) cc_final: -0.0510 (tm)
REVERT: A  993 MET cc_start: 0.8911 (tmm) cc_final: 0.8338 (tmm)
REVERT: A 1071 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8086 (tptt)
REVERT: A 1259 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8363 (t0)
REVERT: A 1422 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6988 (tm-30)
REVERT: A 1439 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6877 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 140
  average time/residue: 0.0578
  time to fit residues: 12.9143
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  577 ILE
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  998 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1071 LYS
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1115 LEU
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 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1439 THR
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    0.1980
   chunk 92 optimal weight:    0.0000
   chunk 95 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3789 r_free = 0.3789 target = 0.128026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.101022 restraints weight = 18108.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.103731 restraints weight = 8887.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.105483 restraints weight = 5307.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.106454 restraints weight = 3731.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107106 restraints weight = 2978.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3645

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= 0.127
  Angle     :  0.572  13.295  11884  Z= 0.273
  Chirality :  0.041   0.296   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  8.134 152.328   1248
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.57 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.25), residues: 1150
  helix:  2.20 (0.18), residues: 789
  sheet: -0.34 (0.82), residues: 50
  loop :  0.15 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1382 
 TYR   0.028   0.001   TYR A1143 
 PHE   0.027   0.001   PHE A 583 
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A1065 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 8678)
  covalent geometry    : angle       0.57244 /  0.27 (11884)
  hydrogen bonds       : bond        0.03840 /  2.55 (  586)
  hydrogen bonds       : angle       3.94757 /  2.91 ( 1710)

*********************** 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
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  219 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7700 (t80)
REVERT: A  239 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8404 (m90)
REVERT: A  823 TYR cc_start: 0.5965 (t80) cc_final: 0.5707 (t80)
REVERT: A  892 LEU cc_start: -0.0108 (OUTLIER) cc_final: -0.0529 (tm)
REVERT: A  993 MET cc_start: 0.8930 (tmm) cc_final: 0.8477 (tmm)
REVERT: A 1071 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7986 (tptt)
REVERT: A 1259 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8413 (t0)
REVERT: A 1352 SER cc_start: 0.9497 (t) cc_final: 0.9251 (p)
REVERT: A 1422 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7144 (tm-30)
REVERT: A 1439 THR cc_start: 0.7156 (OUTLIER) cc_final: 0.6913 (p)
  outliers start: 32
  outliers final: 22
  residues processed: 141
  average time/residue: 0.0617
  time to fit residues: 13.9048
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  761 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  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 1071 LYS
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 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1439 THR
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 66 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    0.1980
   chunk 95 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3811 r_free = 0.3811 target = 0.129715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.102664 restraints weight = 17765.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105385 restraints weight = 8693.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.107214 restraints weight = 5173.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.108147 restraints weight = 3590.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.108840 restraints weight = 2884.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8678  Z= 0.112
  Angle     :  0.570  14.472  11884  Z= 0.268
  Chirality :  0.040   0.295   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  8.117 154.891   1248
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.80 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.25), residues: 1150
  helix:  2.32 (0.19), residues: 782
  sheet: -0.24 (0.83), residues: 50
  loop :  0.18 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1218 
 TYR   0.026   0.001   TYR A1143 
 PHE   0.028   0.001   PHE A 583 
 TRP   0.008   0.001   TRP A 507 
 HIS   0.003   0.000   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 8678)
  covalent geometry    : angle       0.56972 /  0.27 (11884)
  hydrogen bonds       : bond        0.03679 /  2.43 (  586)
  hydrogen bonds       : angle       3.86630 /  2.85 ( 1710)

*********************** 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
  152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7702 (t80)
REVERT: A  239 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.8359 (m90)
REVERT: A  714 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7205 (mt)
REVERT: A  823 TYR cc_start: 0.5939 (t80) cc_final: 0.5687 (t80)
REVERT: A  892 LEU cc_start: -0.0108 (OUTLIER) cc_final: -0.0542 (tm)
REVERT: A  993 MET cc_start: 0.8905 (tmm) cc_final: 0.8405 (tmm)
REVERT: A 1071 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7971 (tptt)
REVERT: A 1259 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8396 (t0)
REVERT: A 1352 SER cc_start: 0.9501 (t) cc_final: 0.9256 (p)
REVERT: A 1422 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7084 (tm-30)
REVERT: A 1439 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6921 (p)
  outliers start: 29
  outliers final: 19
  residues processed: 146
  average time/residue: 0.0608
  time to fit residues: 14.2630
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  : 0.323 
-------------------------------------------------------------------------------
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  444 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  761 THR
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  998 LEU
Chi-restraints excluded: chain A residue 1071 LYS
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 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1439 THR
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 110 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3788 r_free = 0.3788 target = 0.127858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.100892 restraints weight = 17995.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.103558 restraints weight = 8866.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105326 restraints weight = 5318.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.106300 restraints weight = 3705.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.106871 restraints weight = 2971.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8678  Z= 0.139
  Angle     :  0.595  14.778  11884  Z= 0.281
  Chirality :  0.040   0.278   1485
  Planarity :  0.003   0.055   1452
  Dihedral  :  8.179 156.935   1248
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.92 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.25), residues: 1150
  helix:  2.27 (0.18), residues: 783
  sheet: -0.21 (0.83), residues: 50
  loop :  0.09 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1382 
 TYR   0.027   0.001   TYR A1143 
 PHE   0.028   0.001   PHE A 583 
 TRP   0.009   0.001   TRP A 507 
 HIS   0.003   0.001   HIS A 555 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 8678)
  covalent geometry    : angle       0.59541 /  0.28 (11884)
  hydrogen bonds       : bond        0.03820 /  2.54 (  586)
  hydrogen bonds       : angle       3.92238 /  2.89 ( 1710)

*********************** 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
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7738 (t80)
REVERT: A  239 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8398 (m90)
REVERT: A  823 TYR cc_start: 0.5940 (t80) cc_final: 0.5642 (t80)
REVERT: A  892 LEU cc_start: -0.0112 (OUTLIER) cc_final: -0.0523 (tm)
REVERT: A  993 MET cc_start: 0.8906 (tmm) cc_final: 0.8366 (tmm)
REVERT: A 1071 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7965 (tptt)
REVERT: A 1259 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8428 (t0)
REVERT: A 1352 SER cc_start: 0.9494 (t) cc_final: 0.9262 (p)
REVERT: A 1422 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7101 (tm-30)
REVERT: A 1439 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6885 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0616
  time to fit residues: 13.7167
Evaluate side-chains
  141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
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  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  761 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  892 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1071 LYS
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 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1439 THR
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 90 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 108 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0870
   chunk 87 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3812 r_free = 0.3812 target = 0.129696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.102698 restraints weight = 17936.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105422 restraints weight = 8765.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.107209 restraints weight = 5223.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.108297 restraints weight = 3635.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.108821 restraints weight = 2871.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8678  Z= 0.116
  Angle     :  0.587  14.939  11884  Z= 0.276
  Chirality :  0.040   0.312   1485
  Planarity :  0.003   0.055   1452
  Dihedral  :  8.181 159.364   1248
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.55 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.25), residues: 1150
  helix:  2.35 (0.18), residues: 782
  sheet: -0.17 (0.83), residues: 50
  loop :  0.04 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1218 
 TYR   0.026   0.001   TYR A1143 
 PHE   0.028   0.001   PHE A 583 
 TRP   0.010   0.001   TRP A 727 
 HIS   0.002   0.000   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 8678)
  covalent geometry    : angle       0.58681 /  0.28 (11884)
  hydrogen bonds       : bond        0.03689 /  2.44 (  586)
  hydrogen bonds       : angle       3.84355 /  2.83 ( 1710)

********************** 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
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7716 (t80)
REVERT: A  239 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8342 (m90)
REVERT: A  823 TYR cc_start: 0.5894 (t80) cc_final: 0.5492 (t80)
REVERT: A  892 LEU cc_start: -0.0105 (OUTLIER) cc_final: -0.0507 (tm)
REVERT: A  993 MET cc_start: 0.8884 (tmm) cc_final: 0.8315 (tmm)
REVERT: A 1056 MET cc_start: 0.7968 (ttm) cc_final: 0.7631 (tmm)
REVERT: A 1071 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7989 (tptt)
REVERT: A 1259 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8428 (t0)
REVERT: A 1323 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7948 (Cg_endo)
REVERT: A 1352 SER cc_start: 0.9496 (t) cc_final: 0.9265 (p)
REVERT: A 1422 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7005 (tm-30)
REVERT: A 1439 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6918 (p)
  outliers start: 30
  outliers final: 22
  residues processed: 140
  average time/residue: 0.0652
  time to fit residues: 14.3836
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  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  761 THR
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 1069 LEU
Chi-restraints excluded: chain A residue 1071 LYS
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 1263 ARG
Chi-restraints excluded: chain A residue 1317 TYR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1422 GLN
Chi-restraints excluded: chain A residue 1439 THR
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 58 optimal weight:   20.0000
   chunk 107 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3820 r_free = 0.3820 target = 0.130084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.103107 restraints weight = 17852.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.105823 restraints weight = 8764.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.107610 restraints weight = 5242.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.108669 restraints weight = 3649.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.109231 restraints weight = 2911.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8678  Z= 0.115
  Angle     :  0.597  15.195  11884  Z= 0.278
  Chirality :  0.040   0.316   1485
  Planarity :  0.003   0.057   1452
  Dihedral  :  8.123 158.705   1248
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.80 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.25), residues: 1150
  helix:  2.44 (0.18), residues: 775
  sheet: -0.05 (0.84), residues: 50
  loop :  0.14 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1218 
 TYR   0.027   0.001   TYR A1143 
 PHE   0.028   0.001   PHE A 583 
 TRP   0.009   0.001   TRP A 507 
 HIS   0.002   0.000   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 8678)
  covalent geometry    : angle       0.59716 /  0.28 (11884)
  hydrogen bonds       : bond        0.03618 /  2.40 (  586)
  hydrogen bonds       : angle       3.82538 /  2.81 ( 1710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1311.04 seconds
wall clock time: 23 minutes 27.30 seconds (1407.30 seconds total)