Starting phenix.real_space_refine
on Sun Mar 17 21:00:47 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/03_2024/7tnk_26012_updated.pdb"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S     136      5.16       5
     Cl      4      4.86       5
     C   12281      2.51       5
     N    3064      2.21       5
     O    3449      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  453": "NH1" <-> "NH2"
    Residue "A PHE  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  545": "NH1" <-> "NH2"
    Residue "A ARG  599": "NH1" <-> "NH2"
    Residue "A ARG  628": "NH1" <-> "NH2"
    Residue "A ARG  684": "NH1" <-> "NH2"
    Residue "A ARG 1036": "NH1" <-> "NH2"
    Residue "B ARG  545": "NH1" <-> "NH2"
    Residue "B ARG  599": "NH1" <-> "NH2"
    Residue "B ARG  628": "NH1" <-> "NH2"
    Residue "B ARG  684": "NH1" <-> "NH2"
    Residue "B ARG  819": "NH1" <-> "NH2"
    Residue "B ARG 1005": "NH1" <-> "NH2"
    Residue "B ARG 1036": "NH1" <-> "NH2"
    Residue "B ARG 1203": "NH1" <-> "NH2"
    Residue "C ARG  545": "NH1" <-> "NH2"
    Residue "C ARG  594": "NH1" <-> "NH2"
    Residue "C ARG  599": "NH1" <-> "NH2"
    Residue "C ARG 1005": "NH1" <-> "NH2"
    Residue "C ARG 1036": "NH1" <-> "NH2"
    Residue "C TYR 1173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  545": "NH1" <-> "NH2"
    Residue "D TYR  549": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  599": "NH1" <-> "NH2"
    Residue "D ARG  628": "NH1" <-> "NH2"
    Residue "D ARG  684": "NH1" <-> "NH2"
    Residue "D ARG  819": "NH1" <-> "NH2"
    Residue "D ARG 1005": "NH1" <-> "NH2"
    Residue "D ARG 1036": "NH1" <-> "NH2"
    Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG 1203": "NH1" <-> "NH2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 18934
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 615, 4783
          Classifications: {'peptide': 615}
          Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 598}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4688
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 4669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 599, 4669
          Classifications: {'peptide': 599}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4688
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 34
          Unusual residues: {'CYZ': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'CYZ': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'CYZ': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'CYZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.20, per 1000 atoms: 0.54
  Number of scatterers: 18934
  At special positions: 0
  Unit cell: (125.33, 114.54, 136.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S     136     16.00
     O    3449      8.00
     N    3064      7.00
     C   12281      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 718 " - pdb=" SG  CYS A 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1039 " - pdb=" SG  CYS A1067 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1066 " - pdb=" SG  CYS A1076 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 718 " - pdb=" SG  CYS B 773 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1039 " - pdb=" SG  CYS B1067 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1066 " - pdb=" SG  CYS B1076 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 718 " - pdb=" SG  CYS C 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1039 " - pdb=" SG  CYS C1067 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1066 " - pdb=" SG  CYS C1076 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 718 " - pdb=" SG  CYS D 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D1039 " - pdb=" SG  CYS D1067 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D1066 " - pdb=" SG  CYS D1076 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.98
  Conformation dependent library (CDL) restraints added in 3.5 seconds
  

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4416

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      88 helices and 22 sheets defined
      49.1% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 424 through 436
    Processing helix  chain 'A' and resid 462 through 468
      removed outlier: 3.850A  pdb=" N   GLU A 466 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 486
      No H-bonds generated for 'chain 'A' and resid 483 through 486'
    Processing helix  chain 'A' and resid 516 through 518
      No H-bonds generated for 'chain 'A' and resid 516 through 518'
    Processing helix  chain 'A' and resid 523 through 544
      removed outlier: 3.706A  pdb=" N   MET A 527 " --> pdb=" O   TYR A 523 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 568
      No H-bonds generated for 'chain 'A' and resid 566 through 568'
    Processing helix  chain 'A' and resid 573 through 584
      removed outlier: 3.583A  pdb=" N   SER A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 624
      removed outlier: 3.766A  pdb=" N   VAL A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A 611 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A 613 " --> pdb=" O   THR A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 641
    Processing helix  chain 'A' and resid 654 through 660
    Processing helix  chain 'A' and resid 665 through 675
    Processing helix  chain 'A' and resid 686 through 696
      removed outlier: 3.819A  pdb=" N   VAL A 693 " --> pdb=" O   GLY A 689 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER A 696 " --> pdb=" O   ARG A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 714
      removed outlier: 3.886A  pdb=" N   ILE A 712 " --> pdb=" O   MET A 708 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU A 713 " --> pdb=" O   ASN A 709 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN A 714 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 755
      removed outlier: 3.528A  pdb=" N   LYS A 752 " --> pdb=" O   LEU A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 767
      removed outlier: 3.866A  pdb=" N   LYS A 765 " --> pdb=" O   LYS A 761 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TRP A 766 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 791
      No H-bonds generated for 'chain 'A' and resid 789 through 791'
    Processing helix  chain 'A' and resid 793 through 819
      removed outlier: 3.687A  pdb=" N   LEU A 808 " --> pdb=" O   GLY A 804 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 813 " --> pdb=" O   VAL A 809 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE A 814 " --> pdb=" O   ALA A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1028
      removed outlier: 3.504A  pdb=" N   PHE A1017 " --> pdb=" O   THR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1095 through 1102
    Processing helix  chain 'A' and resid 1105 through 1125
      removed outlier: 4.024A  pdb=" N   CYS A1120 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE A1121 " --> pdb=" O   GLY A1117 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A1122 " --> pdb=" O   GLY A1118 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLU A1125 " --> pdb=" O   ILE A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1159
      removed outlier: 3.609A  pdb=" N   ASN A1159 " --> pdb=" O   TYR A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1179 through 1205
      removed outlier: 3.637A  pdb=" N   ILE A1187 " --> pdb=" O   ALA A1183 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A1189 " --> pdb=" O   SER A1185 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASP A1202 " --> pdb=" O   HIS A1198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 420
    Processing helix  chain 'B' and resid 425 through 436
    Processing helix  chain 'B' and resid 462 through 469
      removed outlier: 3.527A  pdb=" N   GLU B 466 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 486
      No H-bonds generated for 'chain 'B' and resid 483 through 486'
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 4.088A  pdb=" N   MET B 527 " --> pdb=" O   TYR B 523 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER B 537 " --> pdb=" O   TYR B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 584
      removed outlier: 3.520A  pdb=" N   LEU B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 625
      removed outlier: 3.842A  pdb=" N   VAL B 601 " --> pdb=" O   SER B 597 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER B 614 " --> pdb=" O   LEU B 610 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 624 " --> pdb=" O   LEU B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 660
      removed outlier: 3.864A  pdb=" N   PHE B 659 " --> pdb=" O   THR B 655 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG B 660 " --> pdb=" O   LYS B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 674
    Processing helix  chain 'B' and resid 686 through 695
      removed outlier: 3.956A  pdb=" N   VAL B 693 " --> pdb=" O   GLY B 689 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG B 694 " --> pdb=" O   VAL B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 713
      removed outlier: 3.754A  pdb=" N   GLU B 713 " --> pdb=" O   ASN B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 743 through 755
      removed outlier: 3.857A  pdb=" N   LEU B 748 " --> pdb=" O   THR B 744 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B 749 " --> pdb=" O   PRO B 745 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 766
    Processing helix  chain 'B' and resid 776 through 778
      No H-bonds generated for 'chain 'B' and resid 776 through 778'
    Processing helix  chain 'B' and resid 793 through 819
      removed outlier: 3.877A  pdb=" N   LEU B 805 " --> pdb=" O   GLY B 801 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B 812 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS B 817 " --> pdb=" O   GLU B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1007 through 1028
      removed outlier: 3.918A  pdb=" N   SER B1021 " --> pdb=" O   PHE B1017 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA B1026 " --> pdb=" O   LEU B1022 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B1028 " --> pdb=" O   THR B1024 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1085 through 1088
    Processing helix  chain 'B' and resid 1092 through 1102
      removed outlier: 3.689A  pdb=" N   ARG B1098 " --> pdb=" O   GLU B1094 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA B1099 " --> pdb=" O   TYR B1095 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL B1100 " --> pdb=" O   PHE B1096 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1105 through 1126
      removed outlier: 3.745A  pdb=" N   LEU B1114 " --> pdb=" O   SER B1110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1133 through 1160
      removed outlier: 3.554A  pdb=" N   PHE B1141 " --> pdb=" O   ALA B1137 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER B1143 " --> pdb=" O   ILE B1139 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA B1144 " --> pdb=" O   PHE B1140 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B1155 " --> pdb=" O   GLY B1151 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN B1159 " --> pdb=" O   TYR B1155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1177 through 1191
      removed outlier: 3.517A  pdb=" N   PHE B1186 " --> pdb=" O   GLY B1182 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA B1189 " --> pdb=" O   SER B1185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1193 through 1203
      removed outlier: 3.683A  pdb=" N   VAL B1197 " --> pdb=" O   GLY B1193 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS B1198 " --> pdb=" O   VAL B1194 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   MET B1199 " --> pdb=" O   LEU B1195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1205 through 1208
      No H-bonds generated for 'chain 'B' and resid 1205 through 1208'
    Processing helix  chain 'C' and resid 417 through 419
      No H-bonds generated for 'chain 'C' and resid 417 through 419'
    Processing helix  chain 'C' and resid 424 through 436
    Processing helix  chain 'C' and resid 462 through 468
    Processing helix  chain 'C' and resid 483 through 488
      removed outlier: 3.805A  pdb=" N   VAL C 488 " --> pdb=" O   VAL C 484 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 523 through 543
      removed outlier: 3.668A  pdb=" N   MET C 527 " --> pdb=" O   TYR C 523 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   CYS C 528 " --> pdb=" O   GLU C 524 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL C 538 " --> pdb=" O   ILE C 534 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL C 539 " --> pdb=" O   GLY C 535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 566 through 568
      No H-bonds generated for 'chain 'C' and resid 566 through 568'
    Processing helix  chain 'C' and resid 573 through 584
    Processing helix  chain 'C' and resid 597 through 629
      removed outlier: 3.645A  pdb=" N   VAL C 601 " --> pdb=" O   SER C 597 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY C 602 " --> pdb=" O   GLY C 598 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL C 604 " --> pdb=" O   ILE C 600 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TRP C 606 " --> pdb=" O   GLY C 602 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL C 626 " --> pdb=" O   ALA C 622 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ARG C 628 " --> pdb=" O   LEU C 624 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 640
    Processing helix  chain 'C' and resid 654 through 660
      removed outlier: 3.732A  pdb=" N   ARG C 660 " --> pdb=" O   LYS C 656 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 665 through 675
      removed outlier: 4.103A  pdb=" N   MET C 670 " --> pdb=" O   VAL C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 686 through 694
      removed outlier: 3.510A  pdb=" N   ALA C 691 " --> pdb=" O   ALA C 687 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL C 693 " --> pdb=" O   GLY C 689 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG C 694 " --> pdb=" O   VAL C 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 706 through 714
      removed outlier: 3.723A  pdb=" N   GLN C 714 " --> pdb=" O   GLU C 710 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 743 through 756
      removed outlier: 3.746A  pdb=" N   LEU C 751 " --> pdb=" O   ASN C 747 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 758 through 766
      removed outlier: 4.294A  pdb=" N   TRP C 766 " --> pdb=" O   LEU C 762 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 819
      removed outlier: 3.819A  pdb=" N   LEU C 808 " --> pdb=" O   GLY C 804 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL C 809 " --> pdb=" O   LEU C 805 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE C 814 " --> pdb=" O   ALA C 810 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   CYS C 815 " --> pdb=" O   LEU C 811 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1005 through 1027
      removed outlier: 3.714A  pdb=" N   MET C1009 " --> pdb=" O   GLY C1006 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C1011 " --> pdb=" O   GLN C1008 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ALA C1016 " --> pdb=" O   THR C1013 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE C1017 " --> pdb=" O   VAL C1014 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA C1019 " --> pdb=" O   ALA C1016 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER C1021 " --> pdb=" O   ALA C1018 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE C1025 " --> pdb=" O   LEU C1022 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL C1027 " --> pdb=" O   THR C1024 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1094 through 1102
      removed outlier: 3.610A  pdb=" N   ALA C1099 " --> pdb=" O   TYR C1095 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA C1102 " --> pdb=" O   ARG C1098 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1106 through 1124
      removed outlier: 3.625A  pdb=" N   VAL C1111 " --> pdb=" O   PRO C1107 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER C1124 " --> pdb=" O   CYS C1120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1133 through 1157
      removed outlier: 3.578A  pdb=" N   ILE C1139 " --> pdb=" O   LEU C1135 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   PHE C1140 " --> pdb=" O   SER C1136 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE C1150 " --> pdb=" O   LEU C1146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1180 through 1207
      removed outlier: 3.573A  pdb=" N   LEU C1195 " --> pdb=" O   MET C1191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 417 through 419
      No H-bonds generated for 'chain 'D' and resid 417 through 419'
    Processing helix  chain 'D' and resid 424 through 435
      removed outlier: 3.550A  pdb=" N   GLU D 431 " --> pdb=" O   ASP D 427 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 462 through 468
    Processing helix  chain 'D' and resid 483 through 486
      No H-bonds generated for 'chain 'D' and resid 483 through 486'
    Processing helix  chain 'D' and resid 514 through 516
      No H-bonds generated for 'chain 'D' and resid 514 through 516'
    Processing helix  chain 'D' and resid 523 through 544
      removed outlier: 4.209A  pdb=" N   MET D 527 " --> pdb=" O   TYR D 523 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE D 541 " --> pdb=" O   SER D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 573 through 584
      removed outlier: 3.668A  pdb=" N   PHE D 584 " --> pdb=" O   SER D 580 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 596 through 625
      removed outlier: 3.874A  pdb=" N   VAL D 601 " --> pdb=" O   SER D 597 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE D 611 " --> pdb=" O   PHE D 607 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 636 through 639
      No H-bonds generated for 'chain 'D' and resid 636 through 639'
    Processing helix  chain 'D' and resid 654 through 659
    Processing helix  chain 'D' and resid 665 through 676
      removed outlier: 3.830A  pdb=" N   THR D 672 " --> pdb=" O   ASP D 668 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   TYR D 673 " --> pdb=" O   LYS D 669 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 686 through 694
      removed outlier: 3.570A  pdb=" N   VAL D 693 " --> pdb=" O   GLY D 689 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG D 694 " --> pdb=" O   VAL D 690 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 706 through 714
      removed outlier: 3.522A  pdb=" N   TYR D 711 " --> pdb=" O   THR D 707 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN D 714 " --> pdb=" O   GLU D 710 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 742 through 755
      removed outlier: 3.633A  pdb=" N   LEU D 748 " --> pdb=" O   THR D 744 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA D 749 " --> pdb=" O   PRO D 745 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 758 through 767
    Processing helix  chain 'D' and resid 793 through 818
      removed outlier: 3.534A  pdb=" N   ALA D 810 " --> pdb=" O   ALA D 806 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1007 through 1028
      removed outlier: 3.746A  pdb=" N   THR D1024 " --> pdb=" O   PHE D1020 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE D1025 " --> pdb=" O   SER D1021 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY D1028 " --> pdb=" O   THR D1024 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1085 through 1088
      removed outlier: 3.746A  pdb=" N   TYR D1088 " --> pdb=" O   ASP D1085 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1085 through 1088'
    Processing helix  chain 'D' and resid 1092 through 1102
      removed outlier: 4.043A  pdb=" N   PHE D1096 " --> pdb=" O   THR D1092 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL D1100 " --> pdb=" O   PHE D1096 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1105 through 1124
      removed outlier: 4.011A  pdb=" N   SER D1110 " --> pdb=" O   PHE D1106 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL D1111 " --> pdb=" O   PRO D1107 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   CYS D1120 " --> pdb=" O   MET D1116 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE D1121 " --> pdb=" O   GLY D1117 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA D1122 " --> pdb=" O   GLY D1118 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER D1124 " --> pdb=" O   CYS D1120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1133 through 1160
      removed outlier: 4.175A  pdb=" N   PHE D1141 " --> pdb=" O   ALA D1137 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL D1142 " --> pdb=" O   GLY D1138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER D1147 " --> pdb=" O   SER D1143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1177 through 1208
      removed outlier: 3.596A  pdb=" N   PHE D1186 " --> pdb=" O   GLY D1182 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU D1195 " --> pdb=" O   MET D1191 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL D1197 " --> pdb=" O   GLY D1193 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 397 through 399
    Processing sheet with id=  B, first strand: chain 'A' and resid 406 through 408
    Processing sheet with id=  C, first strand: chain 'A' and resid 489 through 491
    Processing sheet with id=  D, first strand: chain 'A' and resid 496 through 498
      removed outlier: 3.894A  pdb=" N   MET A 496 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 720 through 723
      removed outlier: 3.688A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   LYS A 505 " --> pdb=" O   TYR A 700 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   TYR A 700 " --> pdb=" O   LYS A 505 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ALA A 646 " --> pdb=" O   ALA A 701 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   LEU A 703 " --> pdb=" O   ALA A 646 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   GLY A 648 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
      removed outlier: 8.874A  pdb=" N   GLU A 705 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 1064 through 1066
    Processing sheet with id=  G, first strand: chain 'B' and resid 395 through 399
    Processing sheet with id=  H, first strand: chain 'B' and resid 406 through 408
    Processing sheet with id=  I, first strand: chain 'B' and resid 496 through 498
      removed outlier: 4.054A  pdb=" N   MET B 496 " --> pdb=" O   TYR B 732 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'B' and resid 720 through 723
      removed outlier: 3.861A  pdb=" N   ILE B 502 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   LYS B 505 " --> pdb=" O   TYR B 700 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   TYR B 700 " --> pdb=" O   LYS B 505 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA B 646 " --> pdb=" O   ALA B 701 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LEU B 703 " --> pdb=" O   ALA B 646 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLY B 648 " --> pdb=" O   LEU B 703 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   GLU B 705 " --> pdb=" O   GLY B 648 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 1033 through 1036
    Processing sheet with id=  L, first strand: chain 'C' and resid 395 through 399
      removed outlier: 3.874A  pdb=" N   THR C 399 " --> pdb=" O   THR C 443 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'C' and resid 406 through 408
    Processing sheet with id=  N, first strand: chain 'C' and resid 452 through 454
      removed outlier: 3.745A  pdb=" N   ALA C 452 " --> pdb=" O   ASN C 461 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASP C 454 " --> pdb=" O   ILE C 459 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE C 459 " --> pdb=" O   ASP C 454 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'C' and resid 496 through 498
      removed outlier: 3.662A  pdb=" N   MET C 496 " --> pdb=" O   TYR C 732 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'C' and resid 720 through 723
      removed outlier: 4.243A  pdb=" N   ILE C 502 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   LYS C 505 " --> pdb=" O   TYR C 700 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   TYR C 700 " --> pdb=" O   LYS C 505 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA C 646 " --> pdb=" O   ALA C 701 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   LEU C 703 " --> pdb=" O   ALA C 646 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY C 648 " --> pdb=" O   LEU C 703 " (cutoff:3.500A)
      removed outlier: 9.491A  pdb=" N   GLU C 705 " --> pdb=" O   GLY C 648 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'D' and resid 396 through 399
      removed outlier: 6.353A  pdb=" N   LYS D 441 " --> pdb=" O   VAL D 397 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   THR D 399 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   THR D 443 " --> pdb=" O   THR D 399 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  Q
    Processing sheet with id=  R, first strand: chain 'D' and resid 452 through 454
      removed outlier: 3.540A  pdb=" N   ALA D 452 " --> pdb=" O   ASN D 461 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'D' and resid 489 through 491
    Processing sheet with id=  T, first strand: chain 'D' and resid 496 through 498
      removed outlier: 4.000A  pdb=" N   MET D 496 " --> pdb=" O   TYR D 732 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'D' and resid 720 through 722
      removed outlier: 4.496A  pdb=" N   LYS D 505 " --> pdb=" O   TYR D 700 " (cutoff:3.500A)
      removed outlier: 8.587A  pdb=" N   TYR D 700 " --> pdb=" O   LYS D 505 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ALA D 646 " --> pdb=" O   ALA D 701 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   LEU D 703 " --> pdb=" O   ALA D 646 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLY D 648 " --> pdb=" O   LEU D 703 " (cutoff:3.500A)
      removed outlier: 9.358A  pdb=" N   GLU D 705 " --> pdb=" O   GLY D 648 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'D' and resid 1033 through 1036
      removed outlier: 3.864A  pdb=" N   LEU D1033 " --> pdb=" O   SER D1060 " (cutoff:3.500A)

    783 hydrogen bonds defined for protein.
    2289 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.81

  Time building geometry restraints manager: 8.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5633
        1.34 -     1.46: 4459
        1.46 -     1.58: 9039
        1.58 -     1.70: 8
        1.70 -     1.82: 220
  Bond restraints: 19359
  Sorted by residual:
  bond pdb=" CA  ASP D1091 "
       pdb=" CB  ASP D1091 "
    ideal  model  delta    sigma   weight residual
    1.524  1.557 -0.034 1.30e-02 5.92e+03 6.72e+00
  bond pdb=" C   SER A 631 "
       pdb=" N   PRO A 632 "
    ideal  model  delta    sigma   weight residual
    1.333  1.369 -0.036 1.44e-02 4.82e+03 6.25e+00
  bond pdb=" N   ASN A1053 "
       pdb=" CA  ASN A1053 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.02e+00
  bond pdb=" C   ASP B 519 "
       pdb=" N   PRO B 520 "
    ideal  model  delta    sigma   weight residual
    1.337  1.358 -0.021 9.80e-03 1.04e+04 4.64e+00
  bond pdb=" N3  CYZ A1302 "
       pdb=" S2  CYZ A1302 "
    ideal  model  delta    sigma   weight residual
    1.644  1.602  0.042 2.00e-02 2.50e+03 4.38e+00
  ... (remaining 19354 not shown)

  Histogram of bond angle deviations from ideal:
       93.28 -   101.59: 98
      101.59 -   109.90: 2746
      109.90 -   118.20: 11921
      118.20 -   126.51: 11107
      126.51 -   134.82: 282
  Bond angle restraints: 26154
  Sorted by residual:
  angle pdb=" C   VAL A1056 "
        pdb=" N   MET A1057 "
        pdb=" CA  MET A1057 "
      ideal   model   delta    sigma   weight residual
     121.54  132.51  -10.97 1.91e+00 2.74e-01 3.30e+01
  angle pdb=" C   GLU B 772 "
        pdb=" N   CYS B 773 "
        pdb=" CA  CYS B 773 "
      ideal   model   delta    sigma   weight residual
     121.54  132.22  -10.68 1.91e+00 2.74e-01 3.13e+01
  angle pdb=" N   ASN B1132 "
        pdb=" CA  ASN B1132 "
        pdb=" C   ASN B1132 "
      ideal   model   delta    sigma   weight residual
     113.61  105.90    7.71 1.50e+00 4.44e-01 2.64e+01
  angle pdb=" C   GLU C1089 "
        pdb=" N   ALA C1090 "
        pdb=" CA  ALA C1090 "
      ideal   model   delta    sigma   weight residual
     120.44  127.06   -6.62 1.30e+00 5.92e-01 2.60e+01
  angle pdb=" C   GLY C 771 "
        pdb=" N   GLU C 772 "
        pdb=" CA  GLU C 772 "
      ideal   model   delta    sigma   weight residual
     121.54  131.07   -9.53 1.91e+00 2.74e-01 2.49e+01
  ... (remaining 26149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.41: 11066
       24.41 -    48.82: 352
       48.82 -    73.23: 15
       73.23 -    97.64: 9
       97.64 -   122.05: 7
  Dihedral angle restraints: 11449
    sinusoidal: 4522
      harmonic: 6927
  Sorted by residual:
  dihedral pdb=" CB  CYS A 718 "
           pdb=" SG  CYS A 718 "
           pdb=" SG  CYS A 773 "
           pdb=" CB  CYS A 773 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.42  -87.58     1      1.00e+01 1.00e-02 9.19e+01
  dihedral pdb=" CA  ALA A 775 "
           pdb=" C   ALA A 775 "
           pdb=" N   LYS A 776 "
           pdb=" CA  LYS A 776 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.71   47.29     0      5.00e+00 4.00e-02 8.94e+01
  dihedral pdb=" CA  LYS B 509 "
           pdb=" C   LYS B 509 "
           pdb=" N   SER B 510 "
           pdb=" CA  SER B 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.48  -44.52     0      5.00e+00 4.00e-02 7.93e+01
  ... (remaining 11446 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2185
       0.052 -    0.105: 584
       0.105 -    0.157: 129
       0.157 -    0.209: 19
       0.209 -    0.261: 8
  Chirality restraints: 2925
  Sorted by residual:
  chirality pdb=" C8  CYZ D1301 "
            pdb=" C1  CYZ D1301 "
            pdb=" N1  CYZ D1301 "
            pdb=" N2  CYZ D1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.46   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  ILE B1079 "
            pdb=" CA  ILE B1079 "
            pdb=" CG1 ILE B1079 "
            pdb=" CG2 ILE B1079 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" C8  CYZ C1301 "
            pdb=" C1  CYZ C1301 "
            pdb=" N1  CYZ C1301 "
            pdb=" N2  CYZ C1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.45   -0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 2922 not shown)

  Planarity restraints: 3209
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 509 "    0.017 2.00e-02 2.50e+03   3.53e-02 1.24e+01
        pdb=" C   LYS B 509 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   LYS B 509 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER B 510 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D1106 "    0.050 5.00e-02 4.00e+02   7.57e-02 9.16e+00
        pdb=" N   PRO D1107 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO D1107 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO D1107 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 744 "   -0.050 5.00e-02 4.00e+02   7.41e-02 8.80e+00
        pdb=" N   PRO B 745 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO B 745 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 745 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 3206 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 4442
        2.78 -     3.31: 17744
        3.31 -     3.84: 30920
        3.84 -     4.37: 36753
        4.37 -     4.90: 60322
  Nonbonded interactions: 150181
  Sorted by model distance:
  nonbonded pdb=" O   PHE D1106 "
            pdb=" OG  SER D1147 "
     model   vdw
     2.244 2.440
  nonbonded pdb=" OG1 THR C 643 "
            pdb=" OD1 ASP D 777 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" O   GLU A 637 "
            pdb=" OG  SER A 640 "
     model   vdw
     2.266 2.440
  nonbonded pdb=" OG1 THR B1065 "
            pdb=" O   LYS B1077 "
     model   vdw
     2.280 2.440
  nonbonded pdb=" O   ILE D1025 "
            pdb=" OG1 THR D1029 "
     model   vdw
     2.292 2.440
  ... (remaining 150176 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 394 through 564 or resid 566 through 1042 or resid 1056 th \ 
rough 1161 or resid 1169 through 1208 or resid 1302))
  selection = (chain 'B' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or  \ 
resid 1301))
  selection = chain 'C'
  selection = (chain 'D' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or  \ 
resid 1301))
}

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:             3.890
  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:             0.000
  Extract box with map and model:          7.590
  Check model and map are aligned:         0.300
  Set scattering table:                    0.160
  Process input model:                     51.780
  Find NCS groups from input model:        1.410
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
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   0.079  19359  Z= 0.335
  Angle     :  1.011  15.267  26154  Z= 0.572
  Chirality :  0.052   0.261   2925
  Planarity :  0.006   0.076   3209
  Dihedral  : 11.811 122.047   6997
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.04 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  4.36 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.97 (0.12), residues: 2380
  helix: -3.73 (0.07), residues: 1242
  sheet: -1.99 (0.38), residues: 162
  loop : -2.69 (0.16), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A1177 
 HIS   0.006   0.001   HIS B1204 
 PHE   0.038   0.002   PHE C1082 
 TYR   0.042   0.003   TYR C1031 
 ARG   0.008   0.001   ARG D 628 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  666 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 658
  time to evaluate  : 2.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7676 (ttp80)
REVERT: A  573 ILE cc_start: 0.7831 (pt) cc_final: 0.7518 (mt)
REVERT: A  610 LEU cc_start: 0.9201 (tp) cc_final: 0.8990 (tp)
REVERT: A  644 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7622 (mp0)
REVERT: A  670 MET cc_start: 0.8182 (mtp) cc_final: 0.7981 (mtt)
REVERT: A  730 LYS cc_start: 0.8202 (mttt) cc_final: 0.7874 (mmmm)
REVERT: A  800 VAL cc_start: 0.9121 (t) cc_final: 0.8892 (p)
REVERT: A 1020 PHE cc_start: 0.7907 (t80) cc_final: 0.7352 (t80)
REVERT: A 1025 ILE cc_start: 0.9065 (mm) cc_final: 0.8864 (mt)
REVERT: A 1031 TYR cc_start: 0.6504 (p90) cc_final: 0.5637 (p90)
REVERT: A 1155 TYR cc_start: 0.8062 (t80) cc_final: 0.7709 (t80)
REVERT: A 1177 TRP cc_start: 0.5743 (p-90) cc_final: 0.4416 (m-10)
REVERT: A 1190 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8612 (mm-30)
REVERT: A 1191 MET cc_start: 0.7682 (tpt) cc_final: 0.7169 (mmt)
REVERT: A 1205 LYS cc_start: 0.7558 (mtmt) cc_final: 0.6999 (tptp)
REVERT: B  399 THR cc_start: 0.8625 (p) cc_final: 0.8388 (t)
REVERT: B  425 CYS cc_start: 0.8636 (m) cc_final: 0.8075 (p)
REVERT: B  428 LEU cc_start: 0.8694 (tp) cc_final: 0.8454 (tp)
REVERT: B  434 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7876 (tttm)
REVERT: B  444 ILE cc_start: 0.8093 (mm) cc_final: 0.7538 (mt)
REVERT: B  474 ILE cc_start: 0.9096 (tt) cc_final: 0.8761 (mm)
REVERT: B  498 LEU cc_start: 0.8975 (pt) cc_final: 0.8654 (pt)
REVERT: B  527 MET cc_start: 0.7366 (ttt) cc_final: 0.6908 (tpt)
REVERT: B  536 VAL cc_start: 0.8177 (t) cc_final: 0.5901 (p)
REVERT: B  586 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7721 (mm-40)
REVERT: B  600 ILE cc_start: 0.8871 (mt) cc_final: 0.8585 (mt)
REVERT: B  605 TRP cc_start: 0.8307 (t-100) cc_final: 0.7487 (t-100)
REVERT: B  609 THR cc_start: 0.9033 (p) cc_final: 0.8691 (t)
REVERT: B  697 LYS cc_start: 0.6121 (mmtp) cc_final: 0.5609 (ptmt)
REVERT: B  766 TRP cc_start: 0.5977 (t-100) cc_final: 0.4915 (t-100)
REVERT: B  800 VAL cc_start: 0.9457 (t) cc_final: 0.9180 (p)
REVERT: B 1003 PHE cc_start: 0.3351 (m-10) cc_final: 0.3129 (m-80)
REVERT: B 1011 LEU cc_start: 0.8421 (tp) cc_final: 0.8118 (tt)
REVERT: B 1181 PHE cc_start: 0.5888 (m-10) cc_final: 0.5527 (m-80)
REVERT: B 1186 PHE cc_start: 0.7464 (t80) cc_final: 0.6942 (t80)
REVERT: B 1191 MET cc_start: 0.8126 (mtp) cc_final: 0.7620 (mtm)
REVERT: C  438 PHE cc_start: 0.7204 (p90) cc_final: 0.5703 (p90)
REVERT: C  503 MET cc_start: 0.8424 (ttp) cc_final: 0.7850 (ttp)
REVERT: C  511 LYS cc_start: 0.7518 (pmmt) cc_final: 0.6870 (mptt)
REVERT: C  528 CYS cc_start: 0.8440 (m) cc_final: 0.7905 (m)
REVERT: C  537 SER cc_start: 0.9190 (p) cc_final: 0.8673 (t)
REVERT: C  585 MET cc_start: 0.8843 (mmt) cc_final: 0.8115 (mmt)
REVERT: C  629 MET cc_start: 0.8386 (mtp) cc_final: 0.7629 (tmm)
REVERT: C  702 TYR cc_start: 0.8041 (t80) cc_final: 0.7679 (t80)
REVERT: C  764 ASN cc_start: 0.8181 (m-40) cc_final: 0.7872 (m-40)
REVERT: C 1009 MET cc_start: 0.8701 (tpp) cc_final: 0.8473 (tpt)
REVERT: C 1030 ASP cc_start: 0.6674 (p0) cc_final: 0.6424 (m-30)
REVERT: C 1064 ARG cc_start: 0.7313 (mpp80) cc_final: 0.6554 (ttt180)
REVERT: C 1141 PHE cc_start: 0.8818 (m-10) cc_final: 0.8550 (m-80)
REVERT: C 1153 ILE cc_start: 0.9546 (mt) cc_final: 0.9205 (mm)
REVERT: C 1180 TYR cc_start: 0.8577 (m-80) cc_final: 0.8124 (m-10)
REVERT: D  431 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7738 (mm-30)
REVERT: D  434 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8308 (mtpt)
REVERT: D  489 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (pp)
REVERT: D  503 MET cc_start: 0.8169 (ttm) cc_final: 0.7543 (ptm)
REVERT: D  505 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7290 (pptt)
REVERT: D  527 MET cc_start: 0.7993 (ptp) cc_final: 0.7694 (mtt)
REVERT: D  537 SER cc_start: 0.8796 (p) cc_final: 0.8078 (t)
REVERT: D  541 PHE cc_start: 0.8441 (t80) cc_final: 0.8156 (t80)
REVERT: D  573 ILE cc_start: 0.9407 (tp) cc_final: 0.9177 (tt)
REVERT: D  580 SER cc_start: 0.8574 (m) cc_final: 0.8138 (m)
REVERT: D  601 VAL cc_start: 0.9504 (t) cc_final: 0.9297 (p)
REVERT: D  629 MET cc_start: 0.5223 (pmt) cc_final: 0.4838 (mmm)
REVERT: D  713 GLU cc_start: 0.7875 (tt0) cc_final: 0.7624 (tm-30)
REVERT: D  714 GLN cc_start: 0.8376 (mm110) cc_final: 0.7865 (mm110)
REVERT: D  752 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8675 (tptt)
REVERT: D 1038 VAL cc_start: 0.7192 (t) cc_final: 0.6779 (m)
REVERT: D 1062 LEU cc_start: 0.4783 (tp) cc_final: 0.4542 (tp)
REVERT: D 1131 HIS cc_start: 0.6296 (m90) cc_final: 0.5989 (m90)
REVERT: D 1134 ILE cc_start: 0.6307 (mp) cc_final: 0.6097 (mm)
REVERT: D 1204 HIS cc_start: 0.7640 (m170) cc_final: 0.7152 (t-170)
REVERT: D 1205 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7489 (mttm)
  outliers start: 8
  outliers final: 0
  residues processed: 662
  average time/residue: 0.3079
  time to fit residues: 307.5193
Evaluate side-chains
  402 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 401
  time to evaluate  : 2.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 202 optimal weight:    0.9980
   chunk 181 optimal weight:    7.9990
   chunk 100 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   chunk 122 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 188 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   chunk 217 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 575 ASN
B 791 ASN
B1171 ASN
** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 418 ASN
C 508 GLN
C 586 GLN
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 791 ASN
C1171 ASN
C1204 HIS
D 435 HIS
** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1131 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  19359  Z= 0.188
  Angle     :  0.602   7.964  26154  Z= 0.323
  Chirality :  0.041   0.173   2925
  Planarity :  0.005   0.094   3209
  Dihedral  :  8.899 109.340   2716
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.87 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.15), residues: 2380
  helix: -1.43 (0.12), residues: 1267
  sheet: -1.65 (0.39), residues: 164
  loop : -2.22 (0.18), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1177 
 HIS   0.005   0.001   HIS A1059 
 PHE   0.022   0.001   PHE C 682 
 TYR   0.024   0.001   TYR C1031 
 ARG   0.020   0.001   ARG B 453 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  524 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 521
  time to evaluate  : 2.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 SER cc_start: 0.9129 (m) cc_final: 0.8745 (t)
REVERT: A  730 LYS cc_start: 0.8391 (mttt) cc_final: 0.8165 (mtpp)
REVERT: A  764 ASN cc_start: 0.8790 (m-40) cc_final: 0.8538 (m110)
REVERT: A  808 LEU cc_start: 0.8875 (tp) cc_final: 0.8620 (mm)
REVERT: A 1004 ASP cc_start: 0.7734 (t0) cc_final: 0.7231 (m-30)
REVERT: A 1007 VAL cc_start: 0.8729 (t) cc_final: 0.8444 (t)
REVERT: A 1020 PHE cc_start: 0.7683 (t80) cc_final: 0.7273 (t80)
REVERT: A 1032 TRP cc_start: 0.7512 (m100) cc_final: 0.6355 (m100)
REVERT: A 1191 MET cc_start: 0.7594 (tpt) cc_final: 0.7180 (mmt)
REVERT: B  399 THR cc_start: 0.8715 (p) cc_final: 0.8404 (t)
REVERT: B  425 CYS cc_start: 0.8513 (m) cc_final: 0.7899 (p)
REVERT: B  428 LEU cc_start: 0.8700 (tp) cc_final: 0.8455 (tp)
REVERT: B  434 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7920 (tptp)
REVERT: B  444 ILE cc_start: 0.8096 (mm) cc_final: 0.7660 (mt)
REVERT: B  474 ILE cc_start: 0.9075 (tt) cc_final: 0.8774 (mm)
REVERT: B  498 LEU cc_start: 0.8708 (pt) cc_final: 0.8397 (pt)
REVERT: B  527 MET cc_start: 0.7334 (ttt) cc_final: 0.6724 (tpt)
REVERT: B  540 LEU cc_start: 0.9210 (tt) cc_final: 0.8861 (tt)
REVERT: B  586 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8192 (mm-40)
REVERT: B  613 ILE cc_start: 0.9143 (mm) cc_final: 0.8913 (mm)
REVERT: B  684 ARG cc_start: 0.6369 (ptp90) cc_final: 0.5854 (mmm160)
REVERT: B  697 LYS cc_start: 0.6036 (mmtp) cc_final: 0.5527 (ptmm)
REVERT: B  766 TRP cc_start: 0.5570 (t-100) cc_final: 0.4810 (t-100)
REVERT: B  768 TYR cc_start: 0.7965 (m-10) cc_final: 0.7463 (m-80)
REVERT: B 1003 PHE cc_start: 0.3586 (m-10) cc_final: 0.3325 (m-80)
REVERT: B 1181 PHE cc_start: 0.5773 (m-10) cc_final: 0.5565 (m-80)
REVERT: B 1191 MET cc_start: 0.8112 (mtp) cc_final: 0.7186 (tpp)
REVERT: C  399 THR cc_start: 0.7624 (t) cc_final: 0.7378 (t)
REVERT: C  406 VAL cc_start: 0.9284 (t) cc_final: 0.8784 (m)
REVERT: C  528 CYS cc_start: 0.7962 (m) cc_final: 0.7338 (m)
REVERT: C  606 TRP cc_start: 0.8353 (m-10) cc_final: 0.8095 (m-10)
REVERT: C  629 MET cc_start: 0.8372 (mtp) cc_final: 0.7627 (tmm)
REVERT: C  639 LEU cc_start: 0.8683 (tp) cc_final: 0.8456 (tp)
REVERT: C  760 ASP cc_start: 0.8471 (t70) cc_final: 0.7916 (t0)
REVERT: C 1009 MET cc_start: 0.8420 (tpp) cc_final: 0.8176 (tpt)
REVERT: C 1030 ASP cc_start: 0.6597 (p0) cc_final: 0.6281 (m-30)
REVERT: C 1062 LEU cc_start: 0.7613 (tp) cc_final: 0.6751 (pt)
REVERT: C 1064 ARG cc_start: 0.7191 (mpp80) cc_final: 0.6486 (ttt-90)
REVERT: C 1153 ILE cc_start: 0.9382 (mt) cc_final: 0.9081 (mm)
REVERT: C 1195 LEU cc_start: 0.8218 (tt) cc_final: 0.7956 (mm)
REVERT: D  431 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7772 (mm-30)
REVERT: D  434 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8221 (mtpt)
REVERT: D  509 LYS cc_start: 0.6468 (ptpp) cc_final: 0.6022 (mmpt)
REVERT: D  537 SER cc_start: 0.8957 (p) cc_final: 0.8711 (t)
REVERT: D  549 TYR cc_start: 0.5968 (p90) cc_final: 0.4724 (t80)
REVERT: D  713 GLU cc_start: 0.8289 (tt0) cc_final: 0.7832 (tm-30)
REVERT: D  714 GLN cc_start: 0.8549 (mm110) cc_final: 0.7863 (mm-40)
REVERT: D  752 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8476 (tptt)
REVERT: D 1062 LEU cc_start: 0.4855 (tp) cc_final: 0.4505 (tp)
REVERT: D 1131 HIS cc_start: 0.6333 (m-70) cc_final: 0.5890 (m90)
  outliers start: 3
  outliers final: 0
  residues processed: 524
  average time/residue: 0.2713
  time to fit residues: 224.8132
Evaluate side-chains
  368 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 368
  time to evaluate  : 2.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 181 optimal weight:    8.9990
   chunk 148 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 218 optimal weight:    5.9990
   chunk 235 optimal weight:    0.8980
   chunk 194 optimal weight:    2.9990
   chunk 216 optimal weight:    6.9990
   chunk 74 optimal weight:    0.2980
   chunk 175 optimal weight:    1.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 791 ASN
** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 791 ASN
C1008 GLN
D 435 HIS
D 642 GLN
** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1206 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  19359  Z= 0.234
  Angle     :  0.606   8.362  26154  Z= 0.323
  Chirality :  0.041   0.153   2925
  Planarity :  0.004   0.063   3209
  Dihedral  :  8.497 110.484   2716
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  4.16 %
    Favored  : 95.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.16), residues: 2380
  helix: -0.20 (0.14), residues: 1270
  sheet: -1.31 (0.40), residues: 163
  loop : -2.11 (0.18), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1177 
 HIS   0.004   0.001   HIS D 435 
 PHE   0.019   0.002   PHE C1072 
 TYR   0.028   0.002   TYR C1031 
 ARG   0.009   0.001   ARG B 453 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  449 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 448
  time to evaluate  : 1.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  503 MET cc_start: 0.7013 (tmm) cc_final: 0.6746 (tmm)
REVERT: A  537 SER cc_start: 0.9209 (m) cc_final: 0.8930 (t)
REVERT: A  708 MET cc_start: 0.8459 (mmt) cc_final: 0.8072 (mmt)
REVERT: A  710 GLU cc_start: 0.8516 (tt0) cc_final: 0.8313 (tt0)
REVERT: A  730 LYS cc_start: 0.8506 (mttt) cc_final: 0.8225 (mtpp)
REVERT: A  808 LEU cc_start: 0.8759 (tp) cc_final: 0.8550 (mm)
REVERT: A 1007 VAL cc_start: 0.8699 (t) cc_final: 0.8377 (t)
REVERT: A 1177 TRP cc_start: 0.6042 (p-90) cc_final: 0.5735 (p-90)
REVERT: A 1190 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: A 1191 MET cc_start: 0.7673 (tpt) cc_final: 0.7232 (mmt)
REVERT: B  399 THR cc_start: 0.8804 (p) cc_final: 0.8491 (t)
REVERT: B  425 CYS cc_start: 0.8468 (m) cc_final: 0.7901 (p)
REVERT: B  434 LYS cc_start: 0.8279 (ptpt) cc_final: 0.7859 (tptp)
REVERT: B  444 ILE cc_start: 0.8242 (mm) cc_final: 0.7812 (mt)
REVERT: B  474 ILE cc_start: 0.9056 (tt) cc_final: 0.8695 (mm)
REVERT: B  481 ILE cc_start: 0.7038 (mm) cc_final: 0.6770 (mm)
REVERT: B  498 LEU cc_start: 0.8681 (pt) cc_final: 0.8384 (pt)
REVERT: B  527 MET cc_start: 0.7498 (ttt) cc_final: 0.6971 (tpt)
REVERT: B  697 LYS cc_start: 0.6106 (mmtp) cc_final: 0.5635 (ptmm)
REVERT: B  766 TRP cc_start: 0.5619 (t-100) cc_final: 0.4855 (t-100)
REVERT: B  768 TYR cc_start: 0.8000 (m-10) cc_final: 0.7503 (m-80)
REVERT: B 1191 MET cc_start: 0.8028 (mtp) cc_final: 0.7318 (tpp)
REVERT: C  406 VAL cc_start: 0.9322 (t) cc_final: 0.8790 (m)
REVERT: C  540 LEU cc_start: 0.9226 (tt) cc_final: 0.9004 (tt)
REVERT: C  606 TRP cc_start: 0.8406 (m-10) cc_final: 0.8141 (m-10)
REVERT: C  629 MET cc_start: 0.8287 (mtp) cc_final: 0.7658 (tmm)
REVERT: C  643 THR cc_start: 0.6863 (p) cc_final: 0.6631 (p)
REVERT: C  702 TYR cc_start: 0.8327 (t80) cc_final: 0.7839 (t80)
REVERT: C 1030 ASP cc_start: 0.6656 (p0) cc_final: 0.6241 (m-30)
REVERT: C 1064 ARG cc_start: 0.6911 (mpp80) cc_final: 0.6660 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9325 (mt) cc_final: 0.9016 (mm)
REVERT: C 1195 LEU cc_start: 0.8306 (tt) cc_final: 0.8028 (mm)
REVERT: D  537 SER cc_start: 0.8969 (p) cc_final: 0.8694 (t)
REVERT: D  580 SER cc_start: 0.8669 (m) cc_final: 0.8129 (m)
REVERT: D  581 LEU cc_start: 0.8836 (tt) cc_final: 0.8613 (tt)
REVERT: D  597 SER cc_start: 0.9183 (p) cc_final: 0.8909 (p)
REVERT: D  713 GLU cc_start: 0.8231 (tt0) cc_final: 0.7922 (tm-30)
REVERT: D  714 GLN cc_start: 0.8436 (mm110) cc_final: 0.7766 (mm-40)
REVERT: D  752 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8513 (tptt)
REVERT: D 1023 MET cc_start: 0.6940 (ttp) cc_final: 0.6652 (ppp)
REVERT: D 1101 ARG cc_start: 0.7282 (ppt170) cc_final: 0.6933 (ptt180)
REVERT: D 1131 HIS cc_start: 0.6480 (m-70) cc_final: 0.5646 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 448
  average time/residue: 0.2689
  time to fit residues: 191.1905
Evaluate side-chains
  335 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 2.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 215 optimal weight:    3.9990
   chunk 164 optimal weight:    5.9990
   chunk 113 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 104 optimal weight:    0.5980
   chunk 146 optimal weight:    6.9990
   chunk 219 optimal weight:    3.9990
   chunk 231 optimal weight:    7.9990
   chunk 114 optimal weight:    8.9990
   chunk 207 optimal weight:    2.9990
   chunk 62 optimal weight:   50.0000
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 ASN
B 791 ASN
B1171 ASN
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 586 GLN
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 435 HIS
D 791 ASN
D1159 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  19359  Z= 0.331
  Angle     :  0.676  14.817  26154  Z= 0.356
  Chirality :  0.044   0.164   2925
  Planarity :  0.005   0.063   3209
  Dihedral  :  8.652 114.509   2716
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.56 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.16), residues: 2380
  helix:  0.16 (0.14), residues: 1264
  sheet: -1.07 (0.42), residues: 157
  loop : -2.16 (0.18), residues: 959

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B1177 
 HIS   0.005   0.001   HIS A1198 
 PHE   0.036   0.002   PHE D1020 
 TYR   0.030   0.002   TYR C1031 
 ARG   0.006   0.001   ARG B 453 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  435 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 434
  time to evaluate  : 2.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  483 LEU cc_start: 0.8869 (tp) cc_final: 0.8556 (tp)
REVERT: A  537 SER cc_start: 0.9244 (m) cc_final: 0.8912 (t)
REVERT: A  670 MET cc_start: 0.8155 (ttm) cc_final: 0.7847 (mmm)
REVERT: A  730 LYS cc_start: 0.8518 (mttt) cc_final: 0.8224 (mtpp)
REVERT: A 1004 ASP cc_start: 0.8106 (t0) cc_final: 0.7878 (t70)
REVERT: A 1007 VAL cc_start: 0.8687 (t) cc_final: 0.8371 (t)
REVERT: A 1020 PHE cc_start: 0.7581 (t80) cc_final: 0.7373 (t80)
REVERT: A 1190 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: A 1191 MET cc_start: 0.7557 (tpt) cc_final: 0.7149 (mmt)
REVERT: B  399 THR cc_start: 0.8918 (p) cc_final: 0.8538 (t)
REVERT: B  425 CYS cc_start: 0.8496 (m) cc_final: 0.7933 (p)
REVERT: B  434 LYS cc_start: 0.8279 (ptpt) cc_final: 0.7866 (tptp)
REVERT: B  444 ILE cc_start: 0.8356 (mm) cc_final: 0.7873 (mt)
REVERT: B  474 ILE cc_start: 0.9037 (tt) cc_final: 0.8677 (mm)
REVERT: B  481 ILE cc_start: 0.7202 (mm) cc_final: 0.6905 (mm)
REVERT: B  498 LEU cc_start: 0.8726 (pt) cc_final: 0.8500 (pt)
REVERT: B  527 MET cc_start: 0.7441 (ttt) cc_final: 0.6901 (tpp)
REVERT: B  540 LEU cc_start: 0.9180 (tt) cc_final: 0.8953 (tt)
REVERT: B  697 LYS cc_start: 0.6355 (mmtp) cc_final: 0.5918 (ptmm)
REVERT: B  766 TRP cc_start: 0.5658 (t-100) cc_final: 0.4879 (t-100)
REVERT: B  768 TYR cc_start: 0.7922 (m-10) cc_final: 0.7343 (m-80)
REVERT: B 1181 PHE cc_start: 0.6113 (m-10) cc_final: 0.5907 (m-80)
REVERT: B 1186 PHE cc_start: 0.7443 (t80) cc_final: 0.7152 (t80)
REVERT: B 1191 MET cc_start: 0.8038 (mtp) cc_final: 0.7350 (tpp)
REVERT: B 1202 ASP cc_start: 0.8892 (m-30) cc_final: 0.8672 (m-30)
REVERT: C  438 PHE cc_start: 0.6944 (p90) cc_final: 0.5952 (p90)
REVERT: C  629 MET cc_start: 0.8335 (mtp) cc_final: 0.7671 (tmm)
REVERT: C  668 ASP cc_start: 0.9031 (t70) cc_final: 0.8659 (t0)
REVERT: C  702 TYR cc_start: 0.8428 (t80) cc_final: 0.7714 (t80)
REVERT: C  764 ASN cc_start: 0.8303 (m-40) cc_final: 0.8082 (m-40)
REVERT: C 1030 ASP cc_start: 0.6665 (p0) cc_final: 0.6074 (m-30)
REVERT: C 1064 ARG cc_start: 0.6961 (mpp80) cc_final: 0.6624 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9337 (mt) cc_final: 0.9051 (mm)
REVERT: C 1175 TYR cc_start: 0.6937 (m-80) cc_final: 0.6604 (m-80)
REVERT: C 1195 LEU cc_start: 0.8365 (tt) cc_final: 0.8103 (mm)
REVERT: D  509 LYS cc_start: 0.6170 (ptpp) cc_final: 0.5925 (tttp)
REVERT: D  537 SER cc_start: 0.9002 (p) cc_final: 0.8624 (t)
REVERT: D  580 SER cc_start: 0.8590 (m) cc_final: 0.7997 (m)
REVERT: D  629 MET cc_start: 0.4787 (tpt) cc_final: 0.4510 (mmm)
REVERT: D  713 GLU cc_start: 0.8330 (tt0) cc_final: 0.8108 (tm-30)
REVERT: D  752 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8573 (tptt)
REVERT: D 1131 HIS cc_start: 0.6653 (m-70) cc_final: 0.5583 (m90)
REVERT: D 1159 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6284 (t0)
REVERT: D 1191 MET cc_start: 0.8008 (ttt) cc_final: 0.7732 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 435
  average time/residue: 0.2675
  time to fit residues: 184.7523
Evaluate side-chains
  325 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 324
  time to evaluate  : 2.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 193 optimal weight:    0.6980
   chunk 131 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 172 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 197 optimal weight:    1.9990
   chunk 160 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 118 optimal weight:    4.9990
   chunk 208 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
B 791 ASN
** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1008 GLN
** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 435 HIS
D1159 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  19359  Z= 0.212
  Angle     :  0.591  16.016  26154  Z= 0.307
  Chirality :  0.041   0.159   2925
  Planarity :  0.004   0.054   3209
  Dihedral  :  8.238 108.693   2716
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.17), residues: 2380
  helix:  0.53 (0.15), residues: 1275
  sheet: -1.25 (0.42), residues: 157
  loop : -2.02 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A1177 
 HIS   0.003   0.001   HIS A 435 
 PHE   0.022   0.002   PHE D1020 
 TYR   0.034   0.001   TYR C1031 
 ARG   0.005   0.000   ARG B 453 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  452 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 452
  time to evaluate  : 2.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 SER cc_start: 0.9194 (m) cc_final: 0.8915 (t)
REVERT: A  585 MET cc_start: 0.7855 (mmm) cc_final: 0.7376 (mmm)
REVERT: A  708 MET cc_start: 0.8394 (mmt) cc_final: 0.7952 (mmt)
REVERT: A  730 LYS cc_start: 0.8505 (mttt) cc_final: 0.8230 (mtpp)
REVERT: A  796 PHE cc_start: 0.8470 (m-80) cc_final: 0.8218 (m-80)
REVERT: A 1004 ASP cc_start: 0.8139 (t0) cc_final: 0.7937 (t70)
REVERT: A 1007 VAL cc_start: 0.8672 (t) cc_final: 0.8365 (t)
REVERT: A 1020 PHE cc_start: 0.7640 (t80) cc_final: 0.7418 (t80)
REVERT: A 1057 MET cc_start: 0.7177 (mpp) cc_final: 0.6669 (mpp)
REVERT: A 1063 TRP cc_start: 0.7411 (m-90) cc_final: 0.7129 (m-10)
REVERT: A 1190 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8327 (mm-30)
REVERT: A 1191 MET cc_start: 0.7633 (tpt) cc_final: 0.7134 (mmt)
REVERT: B  399 THR cc_start: 0.8730 (p) cc_final: 0.8505 (t)
REVERT: B  434 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7854 (tptp)
REVERT: B  444 ILE cc_start: 0.8297 (mm) cc_final: 0.7896 (mt)
REVERT: B  474 ILE cc_start: 0.9044 (tt) cc_final: 0.8689 (mm)
REVERT: B  524 GLU cc_start: 0.7224 (pm20) cc_final: 0.6966 (pm20)
REVERT: B  527 MET cc_start: 0.7489 (ttt) cc_final: 0.6543 (tpp)
REVERT: B  540 LEU cc_start: 0.9188 (tt) cc_final: 0.8960 (tt)
REVERT: B  642 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: B  697 LYS cc_start: 0.6231 (mmtp) cc_final: 0.5564 (ptmm)
REVERT: B  699 LYS cc_start: 0.7527 (tttp) cc_final: 0.7045 (mmpt)
REVERT: B  766 TRP cc_start: 0.5614 (t-100) cc_final: 0.4870 (t-100)
REVERT: B  768 TYR cc_start: 0.7946 (m-10) cc_final: 0.7387 (m-80)
REVERT: B 1181 PHE cc_start: 0.6217 (m-10) cc_final: 0.5980 (m-80)
REVERT: B 1186 PHE cc_start: 0.7486 (t80) cc_final: 0.7150 (t80)
REVERT: B 1191 MET cc_start: 0.7965 (mtp) cc_final: 0.7338 (tpp)
REVERT: C  406 VAL cc_start: 0.9344 (t) cc_final: 0.8823 (m)
REVERT: C  438 PHE cc_start: 0.6839 (p90) cc_final: 0.5983 (p90)
REVERT: C  503 MET cc_start: 0.8328 (ppp) cc_final: 0.7963 (ppp)
REVERT: C  624 LEU cc_start: 0.8748 (mt) cc_final: 0.8478 (mt)
REVERT: C  629 MET cc_start: 0.8288 (mtp) cc_final: 0.7554 (tmm)
REVERT: C  668 ASP cc_start: 0.9039 (t70) cc_final: 0.8708 (t0)
REVERT: C  670 MET cc_start: 0.8522 (mtm) cc_final: 0.8288 (mtp)
REVERT: C  702 TYR cc_start: 0.8356 (t80) cc_final: 0.7561 (t80)
REVERT: C  789 LEU cc_start: 0.9068 (mp) cc_final: 0.8479 (mp)
REVERT: C 1030 ASP cc_start: 0.6650 (p0) cc_final: 0.6155 (m-30)
REVERT: C 1064 ARG cc_start: 0.6965 (mpp80) cc_final: 0.6664 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9351 (mt) cc_final: 0.9056 (mm)
REVERT: C 1175 TYR cc_start: 0.6781 (m-80) cc_final: 0.6546 (m-80)
REVERT: C 1195 LEU cc_start: 0.8430 (tt) cc_final: 0.8173 (mm)
REVERT: D  405 TYR cc_start: 0.7676 (m-80) cc_final: 0.7455 (m-80)
REVERT: D  537 SER cc_start: 0.8998 (p) cc_final: 0.8727 (t)
REVERT: D  549 TYR cc_start: 0.6144 (p90) cc_final: 0.5251 (t80)
REVERT: D  580 SER cc_start: 0.8580 (m) cc_final: 0.8032 (m)
REVERT: D  752 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8521 (tptt)
REVERT: D 1042 LYS cc_start: 0.6780 (pttp) cc_final: 0.6460 (mmtt)
REVERT: D 1131 HIS cc_start: 0.6630 (m-70) cc_final: 0.5710 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 452
  average time/residue: 0.2635
  time to fit residues: 189.8182
Evaluate side-chains
  346 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 208 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 136 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0770
   chunk 232 optimal weight:    0.0670
   chunk 192 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 121 optimal weight:   10.0000
   overall best weight:    2.6282

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

Flipped N/Q/H residues before XYZ refinement:
B 791 ASN
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 586 GLN
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 435 HIS
D 714 GLN
D1159 ASN
D1204 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  19359  Z= 0.263
  Angle     :  0.632  17.763  26154  Z= 0.328
  Chirality :  0.042   0.163   2925
  Planarity :  0.004   0.053   3209
  Dihedral  :  8.234 109.665   2716
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.17), residues: 2380
  helix:  0.70 (0.15), residues: 1254
  sheet: -1.25 (0.41), residues: 157
  loop : -1.97 (0.19), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1177 
 HIS   0.005   0.001   HIS A1198 
 PHE   0.022   0.002   PHE D1020 
 TYR   0.035   0.002   TYR C1031 
 ARG   0.006   0.001   ARG B 453 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 427
  time to evaluate  : 2.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 SER cc_start: 0.9182 (m) cc_final: 0.8935 (t)
REVERT: A  730 LYS cc_start: 0.8507 (mttt) cc_final: 0.8229 (mtpp)
REVERT: A 1004 ASP cc_start: 0.8289 (t0) cc_final: 0.8078 (t70)
REVERT: A 1007 VAL cc_start: 0.8671 (t) cc_final: 0.8446 (t)
REVERT: A 1020 PHE cc_start: 0.7629 (t80) cc_final: 0.7421 (t80)
REVERT: A 1031 TYR cc_start: 0.6489 (p90) cc_final: 0.6236 (p90)
REVERT: A 1177 TRP cc_start: 0.6033 (p-90) cc_final: 0.5735 (p-90)
REVERT: A 1190 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: A 1191 MET cc_start: 0.7566 (tpt) cc_final: 0.7118 (mmt)
REVERT: B  399 THR cc_start: 0.8752 (p) cc_final: 0.8494 (t)
REVERT: B  434 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7804 (tptp)
REVERT: B  444 ILE cc_start: 0.8486 (mm) cc_final: 0.8111 (mt)
REVERT: B  474 ILE cc_start: 0.9087 (tt) cc_final: 0.8695 (mm)
REVERT: B  481 ILE cc_start: 0.7098 (mm) cc_final: 0.6886 (mm)
REVERT: B  642 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: B  697 LYS cc_start: 0.6333 (mmtp) cc_final: 0.5641 (ptmm)
REVERT: B  699 LYS cc_start: 0.7475 (tttp) cc_final: 0.6974 (mmtm)
REVERT: B  766 TRP cc_start: 0.5784 (t-100) cc_final: 0.4856 (t-100)
REVERT: B  768 TYR cc_start: 0.7939 (m-10) cc_final: 0.7353 (m-80)
REVERT: B 1181 PHE cc_start: 0.6101 (m-10) cc_final: 0.5828 (m-80)
REVERT: B 1186 PHE cc_start: 0.7431 (t80) cc_final: 0.7005 (t80)
REVERT: B 1191 MET cc_start: 0.7919 (mtp) cc_final: 0.7365 (tpp)
REVERT: C  438 PHE cc_start: 0.6934 (p90) cc_final: 0.6045 (p90)
REVERT: C  503 MET cc_start: 0.8371 (ppp) cc_final: 0.7922 (ppp)
REVERT: C  585 MET cc_start: 0.8967 (mmt) cc_final: 0.8181 (mmt)
REVERT: C  629 MET cc_start: 0.8279 (mtp) cc_final: 0.7573 (tmm)
REVERT: C  668 ASP cc_start: 0.9065 (t70) cc_final: 0.8741 (t0)
REVERT: C  702 TYR cc_start: 0.8442 (t80) cc_final: 0.7426 (t80)
REVERT: C  760 ASP cc_start: 0.7946 (t0) cc_final: 0.7448 (t0)
REVERT: C  764 ASN cc_start: 0.8557 (m110) cc_final: 0.8078 (t0)
REVERT: C  789 LEU cc_start: 0.9093 (mp) cc_final: 0.8380 (mp)
REVERT: C 1030 ASP cc_start: 0.6483 (p0) cc_final: 0.5880 (m-30)
REVERT: C 1064 ARG cc_start: 0.7025 (mpp80) cc_final: 0.6686 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9343 (mt) cc_final: 0.9090 (mm)
REVERT: C 1175 TYR cc_start: 0.6768 (m-80) cc_final: 0.6516 (m-80)
REVERT: C 1195 LEU cc_start: 0.8436 (tt) cc_final: 0.8189 (mm)
REVERT: D  537 SER cc_start: 0.9030 (p) cc_final: 0.8751 (t)
REVERT: D  549 TYR cc_start: 0.6275 (p90) cc_final: 0.5408 (t80)
REVERT: D  629 MET cc_start: 0.4797 (tpt) cc_final: 0.4494 (mmm)
REVERT: D  674 MET cc_start: 0.8131 (mmm) cc_final: 0.7827 (mmt)
REVERT: D  752 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8523 (tptt)
REVERT: D 1023 MET cc_start: 0.7135 (ppp) cc_final: 0.6710 (ppp)
REVERT: D 1042 LYS cc_start: 0.6986 (pttp) cc_final: 0.6695 (mmtm)
REVERT: D 1057 MET cc_start: 0.4786 (ttp) cc_final: 0.4551 (ttp)
REVERT: D 1131 HIS cc_start: 0.6665 (m-70) cc_final: 0.5567 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 427
  average time/residue: 0.2729
  time to fit residues: 185.3530
Evaluate side-chains
  328 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 2.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 223 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 132 optimal weight:   20.0000
   chunk 169 optimal weight:   10.0000
   chunk 131 optimal weight:    0.8980
   chunk 195 optimal weight:   10.0000
   chunk 129 optimal weight:    0.9980
   chunk 231 optimal weight:    5.9990
   chunk 144 optimal weight:   10.0000
   chunk 141 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 586 GLN
A 709 ASN
B 791 ASN
** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1131 HIS
D 435 HIS
D1159 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  19359  Z= 0.278
  Angle     :  0.637  15.378  26154  Z= 0.331
  Chirality :  0.042   0.154   2925
  Planarity :  0.004   0.053   3209
  Dihedral  :  8.251 110.942   2716
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.17), residues: 2380
  helix:  0.74 (0.15), residues: 1255
  sheet: -0.98 (0.42), residues: 162
  loop : -2.01 (0.19), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 767 
 HIS   0.007   0.001   HIS D1204 
 PHE   0.018   0.002   PHE C1017 
 TYR   0.033   0.002   TYR C1031 
 ARG   0.006   0.001   ARG A1064 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 416
  time to evaluate  : 2.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 VAL cc_start: 0.8806 (t) cc_final: 0.8605 (t)
REVERT: A  537 SER cc_start: 0.9214 (m) cc_final: 0.8883 (t)
REVERT: A  577 LEU cc_start: 0.8857 (mt) cc_final: 0.8586 (mt)
REVERT: A  730 LYS cc_start: 0.8499 (mttt) cc_final: 0.8230 (mtpp)
REVERT: A 1031 TYR cc_start: 0.6534 (p90) cc_final: 0.6215 (p90)
REVERT: A 1177 TRP cc_start: 0.6118 (p-90) cc_final: 0.5814 (p-90)
REVERT: A 1190 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: A 1191 MET cc_start: 0.7614 (tpt) cc_final: 0.7183 (mmt)
REVERT: B  434 LYS cc_start: 0.8215 (ptpt) cc_final: 0.7819 (tptp)
REVERT: B  474 ILE cc_start: 0.9112 (tt) cc_final: 0.8770 (mm)
REVERT: B  502 ILE cc_start: 0.7286 (mt) cc_final: 0.7021 (mt)
REVERT: B  533 TYR cc_start: 0.8263 (t80) cc_final: 0.8035 (t80)
REVERT: B  642 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: B  697 LYS cc_start: 0.6483 (mmtp) cc_final: 0.5923 (ptmm)
REVERT: B  699 LYS cc_start: 0.7297 (tttp) cc_final: 0.6863 (mmpt)
REVERT: B  755 GLU cc_start: 0.6638 (pt0) cc_final: 0.6301 (tp30)
REVERT: B  766 TRP cc_start: 0.5817 (t-100) cc_final: 0.4990 (t-100)
REVERT: B 1191 MET cc_start: 0.7908 (mtp) cc_final: 0.7120 (tpp)
REVERT: C  438 PHE cc_start: 0.6732 (p90) cc_final: 0.6165 (p90)
REVERT: C  503 MET cc_start: 0.8427 (ppp) cc_final: 0.8148 (ppp)
REVERT: C  629 MET cc_start: 0.8330 (mtp) cc_final: 0.7633 (tmm)
REVERT: C  668 ASP cc_start: 0.9060 (t70) cc_final: 0.8777 (t0)
REVERT: C  702 TYR cc_start: 0.8491 (t80) cc_final: 0.8154 (t80)
REVERT: C  704 LEU cc_start: 0.9090 (pt) cc_final: 0.8756 (pt)
REVERT: C  764 ASN cc_start: 0.8500 (m110) cc_final: 0.7951 (t0)
REVERT: C 1030 ASP cc_start: 0.6629 (p0) cc_final: 0.5972 (m-30)
REVERT: C 1064 ARG cc_start: 0.7149 (mpp80) cc_final: 0.6751 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9339 (mt) cc_final: 0.9080 (mm)
REVERT: C 1175 TYR cc_start: 0.6740 (m-80) cc_final: 0.6486 (m-80)
REVERT: C 1195 LEU cc_start: 0.8482 (tt) cc_final: 0.8243 (mm)
REVERT: D  509 LYS cc_start: 0.6116 (ptpp) cc_final: 0.5832 (tttp)
REVERT: D  537 SER cc_start: 0.9022 (p) cc_final: 0.8763 (t)
REVERT: D  549 TYR cc_start: 0.6302 (p90) cc_final: 0.5453 (t80)
REVERT: D  580 SER cc_start: 0.8631 (m) cc_final: 0.8049 (m)
REVERT: D  629 MET cc_start: 0.4794 (tpt) cc_final: 0.4559 (mmm)
REVERT: D 1042 LYS cc_start: 0.6991 (pttp) cc_final: 0.6761 (mmtp)
REVERT: D 1057 MET cc_start: 0.4782 (ttp) cc_final: 0.4517 (ttp)
REVERT: D 1131 HIS cc_start: 0.6642 (m-70) cc_final: 0.5564 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 416
  average time/residue: 0.2624
  time to fit residues: 175.6904
Evaluate side-chains
  334 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 2.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 143 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   chunk 138 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 147 optimal weight:    0.9990
   chunk 157 optimal weight:    4.9990
   chunk 114 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 181 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 586 GLN
A 709 ASN
B 791 ASN
** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 586 GLN
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1131 HIS
C1204 HIS
D 435 HIS
D 586 GLN
D1159 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  19359  Z= 0.279
  Angle     :  0.640   8.774  26154  Z= 0.334
  Chirality :  0.043   0.189   2925
  Planarity :  0.004   0.053   3209
  Dihedral  :  8.238 109.858   2716
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.17), residues: 2380
  helix:  0.72 (0.15), residues: 1256
  sheet: -1.15 (0.41), residues: 173
  loop : -1.92 (0.19), residues: 951

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1177 
 HIS   0.005   0.001   HIS D1204 
 PHE   0.023   0.002   PHE B1186 
 TYR   0.031   0.002   TYR C1031 
 ARG   0.005   0.001   ARG B 661 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 411
  time to evaluate  : 1.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 VAL cc_start: 0.8802 (t) cc_final: 0.8586 (t)
REVERT: A  537 SER cc_start: 0.9182 (m) cc_final: 0.8891 (t)
REVERT: A  585 MET cc_start: 0.7707 (mmm) cc_final: 0.7395 (mmm)
REVERT: A  730 LYS cc_start: 0.8516 (mttt) cc_final: 0.8249 (mtpp)
REVERT: A 1020 PHE cc_start: 0.7627 (t80) cc_final: 0.7425 (t80)
REVERT: A 1141 PHE cc_start: 0.8551 (m-80) cc_final: 0.8239 (m-80)
REVERT: A 1190 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: A 1191 MET cc_start: 0.7619 (tpt) cc_final: 0.7194 (mmt)
REVERT: B  399 THR cc_start: 0.8396 (p) cc_final: 0.8074 (t)
REVERT: B  434 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7822 (tptp)
REVERT: B  444 ILE cc_start: 0.8300 (mm) cc_final: 0.7804 (mt)
REVERT: B  474 ILE cc_start: 0.9050 (tt) cc_final: 0.8713 (mm)
REVERT: B  642 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7500 (tm-30)
REVERT: B  697 LYS cc_start: 0.6603 (mmtp) cc_final: 0.5958 (ptmm)
REVERT: B  755 GLU cc_start: 0.6651 (pt0) cc_final: 0.6353 (tp30)
REVERT: B  766 TRP cc_start: 0.5834 (t-100) cc_final: 0.4921 (t-100)
REVERT: B  768 TYR cc_start: 0.8109 (m-80) cc_final: 0.7819 (m-80)
REVERT: B 1191 MET cc_start: 0.7590 (mtp) cc_final: 0.7142 (tpp)
REVERT: C  438 PHE cc_start: 0.6651 (p90) cc_final: 0.6090 (p90)
REVERT: C  585 MET cc_start: 0.8993 (mmt) cc_final: 0.8399 (mmt)
REVERT: C  629 MET cc_start: 0.8325 (mtp) cc_final: 0.7639 (tmm)
REVERT: C  668 ASP cc_start: 0.9106 (t70) cc_final: 0.8793 (t0)
REVERT: C  702 TYR cc_start: 0.8555 (t80) cc_final: 0.8211 (t80)
REVERT: C  704 LEU cc_start: 0.9119 (pt) cc_final: 0.8754 (pt)
REVERT: C  764 ASN cc_start: 0.8564 (m110) cc_final: 0.8227 (m110)
REVERT: C 1064 ARG cc_start: 0.7201 (mpp80) cc_final: 0.6601 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9320 (mt) cc_final: 0.9100 (mm)
REVERT: C 1175 TYR cc_start: 0.6683 (m-80) cc_final: 0.6394 (m-80)
REVERT: C 1195 LEU cc_start: 0.8489 (tt) cc_final: 0.8264 (mm)
REVERT: D  509 LYS cc_start: 0.6158 (ptpp) cc_final: 0.5857 (tttp)
REVERT: D  537 SER cc_start: 0.9014 (p) cc_final: 0.8766 (t)
REVERT: D  549 TYR cc_start: 0.6289 (p90) cc_final: 0.5509 (t80)
REVERT: D 1057 MET cc_start: 0.4754 (ttp) cc_final: 0.4465 (ttp)
REVERT: D 1131 HIS cc_start: 0.6652 (m-70) cc_final: 0.5820 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 411
  average time/residue: 0.2742
  time to fit residues: 182.2547
Evaluate side-chains
  317 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 2.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 210 optimal weight:    2.9990
   chunk 221 optimal weight:   20.0000
   chunk 202 optimal weight:    0.0980
   chunk 215 optimal weight:    5.9990
   chunk 129 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 169 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 194 optimal weight:    4.9990
   chunk 203 optimal weight:    0.9980
   chunk 214 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 709 ASN
A 764 ASN
** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 791 ASN
B1131 HIS
B1171 ASN
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1131 HIS
D 714 GLN
D1159 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  19359  Z= 0.153
  Angle     :  0.568   8.568  26154  Z= 0.290
  Chirality :  0.040   0.178   2925
  Planarity :  0.004   0.054   3209
  Dihedral  :  7.688 101.073   2716
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.17), residues: 2380
  helix:  1.05 (0.15), residues: 1262
  sheet: -0.76 (0.44), residues: 155
  loop : -1.80 (0.19), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1177 
 HIS   0.005   0.001   HIS A1059 
 PHE   0.022   0.001   PHE B 517 
 TYR   0.023   0.001   TYR C1031 
 ARG   0.007   0.000   ARG B 661 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  430 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 430
  time to evaluate  : 2.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  469 TYR cc_start: 0.8177 (m-10) cc_final: 0.7857 (m-10)
REVERT: A  483 LEU cc_start: 0.8576 (tp) cc_final: 0.8328 (tp)
REVERT: A  489 ILE cc_start: 0.8622 (pt) cc_final: 0.8387 (pt)
REVERT: A  537 SER cc_start: 0.9192 (m) cc_final: 0.8984 (t)
REVERT: A  585 MET cc_start: 0.7811 (mmm) cc_final: 0.7524 (mmm)
REVERT: A  730 LYS cc_start: 0.8551 (mttt) cc_final: 0.8283 (mtpp)
REVERT: A 1020 PHE cc_start: 0.7660 (t80) cc_final: 0.7457 (t80)
REVERT: A 1031 TYR cc_start: 0.6538 (p90) cc_final: 0.6337 (p90)
REVERT: A 1032 TRP cc_start: 0.7884 (m100) cc_final: 0.7511 (m100)
REVERT: A 1141 PHE cc_start: 0.8550 (m-80) cc_final: 0.8318 (m-80)
REVERT: A 1177 TRP cc_start: 0.6265 (p-90) cc_final: 0.5960 (p-90)
REVERT: A 1190 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8293 (mm-30)
REVERT: A 1191 MET cc_start: 0.7688 (tpt) cc_final: 0.7243 (mmt)
REVERT: B  434 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7753 (tptp)
REVERT: B  444 ILE cc_start: 0.8170 (mm) cc_final: 0.7689 (mt)
REVERT: B  474 ILE cc_start: 0.9112 (tt) cc_final: 0.8778 (mm)
REVERT: B  642 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7475 (pp30)
REVERT: B  697 LYS cc_start: 0.6422 (mmtp) cc_final: 0.5646 (ptmm)
REVERT: B  699 LYS cc_start: 0.7359 (tttp) cc_final: 0.6919 (mmpt)
REVERT: B  755 GLU cc_start: 0.6575 (pt0) cc_final: 0.6355 (tp30)
REVERT: B  766 TRP cc_start: 0.5718 (t-100) cc_final: 0.4972 (t-100)
REVERT: B  768 TYR cc_start: 0.8110 (m-80) cc_final: 0.7846 (m-80)
REVERT: B 1191 MET cc_start: 0.7721 (mtp) cc_final: 0.7136 (tpp)
REVERT: C  424 TYR cc_start: 0.7349 (t80) cc_final: 0.6998 (t80)
REVERT: C  438 PHE cc_start: 0.6751 (p90) cc_final: 0.6133 (p90)
REVERT: C  503 MET cc_start: 0.8619 (ppp) cc_final: 0.7967 (ppp)
REVERT: C  629 MET cc_start: 0.8172 (mtp) cc_final: 0.7650 (tmm)
REVERT: C  702 TYR cc_start: 0.8309 (t80) cc_final: 0.7971 (t80)
REVERT: C  764 ASN cc_start: 0.8430 (m110) cc_final: 0.7867 (t0)
REVERT: C 1030 ASP cc_start: 0.6731 (p0) cc_final: 0.6195 (m-30)
REVERT: C 1064 ARG cc_start: 0.7161 (mpp80) cc_final: 0.6685 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9278 (mt) cc_final: 0.9032 (mm)
REVERT: C 1195 LEU cc_start: 0.8479 (tt) cc_final: 0.8209 (mm)
REVERT: D 1057 MET cc_start: 0.4649 (ttp) cc_final: 0.4402 (ttp)
REVERT: D 1131 HIS cc_start: 0.6572 (m-70) cc_final: 0.5855 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 430
  average time/residue: 0.2636
  time to fit residues: 181.3066
Evaluate side-chains
  332 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 2.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 227 optimal weight:    5.9990
   chunk 139 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 158 optimal weight:    0.5980
   chunk 239 optimal weight:    9.9990
   chunk 220 optimal weight:    4.9990
   chunk 190 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 147 optimal weight:    0.9980
   chunk 116 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 709 ASN
** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 791 ASN
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 435 HIS
C 586 GLN
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1131 HIS
C1204 HIS
D 586 GLN
D1159 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  19359  Z= 0.171
  Angle     :  0.581   9.189  26154  Z= 0.297
  Chirality :  0.041   0.178   2925
  Planarity :  0.004   0.054   3209
  Dihedral  :  7.548 101.261   2716
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.40 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.17), residues: 2380
  helix:  1.21 (0.15), residues: 1255
  sheet: -1.10 (0.42), residues: 161
  loop : -1.79 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B1032 
 HIS   0.006   0.001   HIS D1204 
 PHE   0.024   0.001   PHE A1179 
 TYR   0.025   0.001   TYR C1031 
 ARG   0.004   0.000   ARG A1064 

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

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

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4760 Ramachandran restraints generated.
    2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 416
  time to evaluate  : 2.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 VAL cc_start: 0.8660 (t) cc_final: 0.8456 (t)
REVERT: A  466 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7035 (mm-30)
REVERT: A  469 TYR cc_start: 0.8035 (m-10) cc_final: 0.7640 (m-80)
REVERT: A  670 MET cc_start: 0.8082 (mmp) cc_final: 0.7761 (mmt)
REVERT: A  730 LYS cc_start: 0.8561 (mttt) cc_final: 0.8120 (mtpp)
REVERT: A  764 ASN cc_start: 0.8430 (m-40) cc_final: 0.7962 (m110)
REVERT: A 1031 TYR cc_start: 0.6539 (p90) cc_final: 0.6302 (p90)
REVERT: A 1032 TRP cc_start: 0.7890 (m100) cc_final: 0.7568 (m100)
REVERT: A 1081 HIS cc_start: 0.6741 (m90) cc_final: 0.6527 (m170)
REVERT: A 1177 TRP cc_start: 0.6235 (p-90) cc_final: 0.5965 (p-90)
REVERT: A 1190 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: A 1191 MET cc_start: 0.7632 (tpt) cc_final: 0.7216 (mmt)
REVERT: B  399 THR cc_start: 0.7885 (t) cc_final: 0.7612 (t)
REVERT: B  434 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7817 (tttm)
REVERT: B  444 ILE cc_start: 0.7933 (mm) cc_final: 0.7448 (mt)
REVERT: B  474 ILE cc_start: 0.9081 (tt) cc_final: 0.8765 (mm)
REVERT: B  540 LEU cc_start: 0.9030 (tt) cc_final: 0.8799 (tt)
REVERT: B  642 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7533 (pp30)
REVERT: B  697 LYS cc_start: 0.6424 (mmtp) cc_final: 0.5725 (ptmm)
REVERT: B  699 LYS cc_start: 0.7311 (tttp) cc_final: 0.6941 (mmpt)
REVERT: B  766 TRP cc_start: 0.5748 (t-100) cc_final: 0.4971 (t-100)
REVERT: B  768 TYR cc_start: 0.8094 (m-80) cc_final: 0.7860 (m-80)
REVERT: B 1186 PHE cc_start: 0.7506 (t80) cc_final: 0.7068 (t80)
REVERT: B 1191 MET cc_start: 0.7654 (mtp) cc_final: 0.7208 (tpp)
REVERT: B 1201 ILE cc_start: 0.8246 (pt) cc_final: 0.7881 (tp)
REVERT: C  424 TYR cc_start: 0.7343 (t80) cc_final: 0.6957 (t80)
REVERT: C  438 PHE cc_start: 0.6728 (p90) cc_final: 0.6101 (p90)
REVERT: C  503 MET cc_start: 0.8631 (ppp) cc_final: 0.7741 (ppp)
REVERT: C  629 MET cc_start: 0.8163 (mtp) cc_final: 0.7674 (tmm)
REVERT: C  639 LEU cc_start: 0.8293 (mt) cc_final: 0.7794 (mt)
REVERT: C 1064 ARG cc_start: 0.7154 (mpp80) cc_final: 0.6590 (ttt180)
REVERT: C 1153 ILE cc_start: 0.9271 (mt) cc_final: 0.9023 (mm)
REVERT: C 1195 LEU cc_start: 0.8469 (tt) cc_final: 0.8163 (mm)
REVERT: D  585 MET cc_start: 0.7750 (mmm) cc_final: 0.7445 (mmm)
REVERT: D 1057 MET cc_start: 0.4573 (ttp) cc_final: 0.4346 (ttp)
REVERT: D 1131 HIS cc_start: 0.6692 (m-70) cc_final: 0.5885 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 417
  average time/residue: 0.2676
  time to fit residues: 178.7926
Evaluate side-chains
  332 residues out of total 2020 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 2.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 151 optimal weight:    4.9990
   chunk 202 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 175 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 190 optimal weight:    6.9990
   chunk 79 optimal weight:    0.3980
   chunk 195 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 709 ASN
** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 764 ASN
B 791 ASN
** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1131 HIS
D 586 GLN
D1159 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.097056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.080302 restraints weight = 64622.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.082523 restraints weight = 39345.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.083966 restraints weight = 27457.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  19359  Z= 0.225
  Angle     :  0.605  10.981  26154  Z= 0.311
  Chirality :  0.041   0.172   2925
  Planarity :  0.004   0.053   3209
  Dihedral  :  7.650 104.901   2716
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.17), residues: 2380
  helix:  1.18 (0.15), residues: 1256
  sheet: -1.16 (0.41), residues: 169
  loop : -1.80 (0.19), residues: 955

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 766 
 HIS   0.006   0.001   HIS D1204 
 PHE   0.023   0.002   PHE B1186 
 TYR   0.027   0.002   TYR C1031 
 ARG   0.004   0.000   ARG A1064 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4217.65 seconds
wall clock time: 77 minutes 35.43 seconds (4655.43 seconds total)