Starting phenix.real_space_refine
on Tue Jun 24 18:18:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pkv_20367/06_2025/6pkv_20367.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C   18092      2.51       5
     N    5088      2.21       5
     O    5032      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.37s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 28284
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 886, 5765
          Classifications: {'peptide': 886}
          Incomplete info: {'truncation_to_alanine': 407}
          Link IDs: {'PTRANS': 24, 'TRANS': 861}
          Chain breaks: 16
          Unresolved non-hydrogen bonds: 1501
          Unresolved non-hydrogen angles: 1886
          Unresolved non-hydrogen dihedrals: 1207
          Unresolved non-hydrogen chiralities: 138
          Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 28, 'PHE:plan': 18, 'GLU:plan': 58, 'ARG:plan': 36}
          Unresolved non-hydrogen planarities: 855
    Chain: "A"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1306
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 317
          Unresolved non-hydrogen angles: 409
          Unresolved non-hydrogen dihedrals: 251
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 2, 'UNK:plan-1': 22, 'TRP:plan': 2, 'HIS:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 205
  Restraints were copied for chains:
    C, B, D
  Residues with excluded nonbonded symmetry interactions: 12
    residue:
      pdb=" N   GLU A1272 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU A1272 " occ=0.50
    residue:
      pdb=" N   VAL A1287 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  VAL A1287 " occ=0.50
    residue:
      pdb=" N   VAL A1400 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CG2 VAL A1400 " occ=0.50
    residue:
      pdb=" N   GLU B1272 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B1272 " occ=0.50
    residue:
      pdb=" N   VAL B1287 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  VAL B1287 " occ=0.50
    residue:
      pdb=" N   VAL B1400 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CG2 VAL B1400 " occ=0.50
    residue:
      pdb=" N   GLU C1272 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU C1272 " occ=0.50
    residue:
      pdb=" N   VAL C1287 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  VAL C1287 " occ=0.50
    residue:
      pdb=" N   VAL C1400 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CG2 VAL C1400 " occ=0.50
    residue:
      pdb=" N   GLU D1272 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU D1272 " occ=0.50
    residue:
      pdb=" N   VAL D1287 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  VAL D1287 " occ=0.50
    residue:
      pdb=" N   VAL D1400 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CG2 VAL D1400 " occ=0.50
  Time building chain proxies: 17.60, per 1000 atoms: 0.62
  Number of scatterers: 28284
  At special positions: 0
  Unit cell: (148.174, 148.174, 182.286, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    5032      8.00
     N    5088      7.00
     C   18092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.53
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  8280

  Finding SS restraints...
    Secondary structure from input PDB file:
      192 helices and 12 sheets defined
      65.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 49
      removed outlier: 3.688A  pdb=" N   ASN A  47 " --> pdb=" O   TRP A  43 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   LYS A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 136
    Processing helix  chain 'A' and resid 159 through 177
      removed outlier: 3.607A  pdb=" N   LYS A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS A 165 " --> pdb=" O   HIS A 161 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 201
      removed outlier: 3.728A  pdb=" N   HIS A 193 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 288
    Processing helix  chain 'A' and resid 311 through 322
      removed outlier: 3.896A  pdb=" N   THR A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 354 through 361
    Processing helix  chain 'A' and resid 374 through 387
    Processing helix  chain 'A' and resid 406 through 419
    Processing helix  chain 'A' and resid 426 through 439
      removed outlier: 3.721A  pdb=" N   ARG A 430 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TRP A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 448
      removed outlier: 3.849A  pdb=" N   ALA A 444 " --> pdb=" O   ARG A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 470
      removed outlier: 3.943A  pdb=" N   GLY A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 483
    Processing helix  chain 'A' and resid 485 through 490
    Processing helix  chain 'A' and resid 492 through 502
      removed outlier: 3.989A  pdb=" N   LEU A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 517
    Processing helix  chain 'A' and resid 536 through 548
    Processing helix  chain 'A' and resid 593 through 606
      removed outlier: 3.579A  pdb=" N   ASN A 606 " --> pdb=" O   ALA A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 620 through 639
      removed outlier: 3.893A  pdb=" N   GLU A 638 " --> pdb=" O   LYS A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 672
      removed outlier: 3.629A  pdb=" N   VAL A 664 " --> pdb=" O   GLN A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 681
    Processing helix  chain 'A' and resid 691 through 700
    Processing helix  chain 'A' and resid 701 through 706
      removed outlier: 3.597A  pdb=" N   ILE A 705 " --> pdb=" O   ASP A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 720
    Processing helix  chain 'A' and resid 729 through 737
    Processing helix  chain 'A' and resid 738 through 743
      removed outlier: 4.065A  pdb=" N   ILE A 741 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR A 742 " --> pdb=" O   PRO A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 762
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 808 through 833
    Processing helix  chain 'A' and resid 840 through 865
      removed outlier: 4.008A  pdb=" N   PHE A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 880
    Processing helix  chain 'A' and resid 882 through 902
      removed outlier: 3.543A  pdb=" N   GLN A 902 " --> pdb=" O   ILE A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 927
      removed outlier: 3.716A  pdb=" N   ILE A 920 " --> pdb=" O   CYS A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 932
      removed outlier: 3.791A  pdb=" N   ILE A 932 " --> pdb=" O   ILE A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 935 through 946
      removed outlier: 3.995A  pdb=" N   LYS A 939 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET A 946 " --> pdb=" O   ILE A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 973
      removed outlier: 3.974A  pdb=" N   PHE A 951 " --> pdb=" O   MET A 947 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE A 953 " --> pdb=" O   ASP A 949 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   MET A 954 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE A 955 " --> pdb=" O   PHE A 951 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU A 956 " --> pdb=" O   PHE A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 987
      removed outlier: 3.702A  pdb=" N   VAL A 987 " --> pdb=" O   ILE A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1065
      removed outlier: 3.788A  pdb=" N   THR A1040 " --> pdb=" O   PRO A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1092
      removed outlier: 4.199A  pdb=" N   TYR A1083 " --> pdb=" O   LYS A1079 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   GLU A1084 " --> pdb=" O   PHE A1080 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ARG A1092 " --> pdb=" O   GLU A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1114
      removed outlier: 4.262A  pdb=" N   LEU A1102 " --> pdb=" O   PRO A1098 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1154
    Processing helix  chain 'A' and resid 1158 through 1184
    Processing helix  chain 'A' and resid 1189 through 1208
    Processing helix  chain 'A' and resid 1270 through 1275
    Processing helix  chain 'A' and resid 1370 through 1381
    Processing helix  chain 'A' and resid 1456 through 1467
    Processing helix  chain 'B' and resid 41 through 49
      removed outlier: 3.688A  pdb=" N   ASN B  47 " --> pdb=" O   TRP B  43 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B  48 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   LYS B  49 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 136
    Processing helix  chain 'B' and resid 159 through 177
      removed outlier: 3.608A  pdb=" N   LYS B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS B 165 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 201
      removed outlier: 3.728A  pdb=" N   HIS B 193 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 288
    Processing helix  chain 'B' and resid 311 through 322
      removed outlier: 3.895A  pdb=" N   THR B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 342
    Processing helix  chain 'B' and resid 354 through 361
    Processing helix  chain 'B' and resid 374 through 387
    Processing helix  chain 'B' and resid 406 through 419
    Processing helix  chain 'B' and resid 426 through 439
      removed outlier: 3.721A  pdb=" N   ARG B 430 " --> pdb=" O   HIS B 426 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TRP B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 448
      removed outlier: 3.849A  pdb=" N   ALA B 444 " --> pdb=" O   ARG B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 470
      removed outlier: 3.942A  pdb=" N   GLY B 470 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 483
    Processing helix  chain 'B' and resid 485 through 490
    Processing helix  chain 'B' and resid 492 through 502
      removed outlier: 3.989A  pdb=" N   LEU B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 517
    Processing helix  chain 'B' and resid 536 through 548
    Processing helix  chain 'B' and resid 593 through 606
      removed outlier: 3.578A  pdb=" N   ASN B 606 " --> pdb=" O   ALA B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 618
    Processing helix  chain 'B' and resid 620 through 639
      removed outlier: 3.894A  pdb=" N   GLU B 638 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 672
      removed outlier: 3.630A  pdb=" N   VAL B 664 " --> pdb=" O   GLN B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 681
    Processing helix  chain 'B' and resid 691 through 700
    Processing helix  chain 'B' and resid 701 through 706
      removed outlier: 3.597A  pdb=" N   ILE B 705 " --> pdb=" O   ASP B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 707 through 720
    Processing helix  chain 'B' and resid 729 through 737
    Processing helix  chain 'B' and resid 738 through 743
      removed outlier: 4.065A  pdb=" N   ILE B 741 " --> pdb=" O   PHE B 738 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR B 742 " --> pdb=" O   PRO B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 762
    Processing helix  chain 'B' and resid 799 through 807
    Processing helix  chain 'B' and resid 808 through 833
    Processing helix  chain 'B' and resid 840 through 865
      removed outlier: 4.008A  pdb=" N   PHE B 865 " --> pdb=" O   LEU B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 870 through 880
    Processing helix  chain 'B' and resid 882 through 902
      removed outlier: 3.543A  pdb=" N   GLN B 902 " --> pdb=" O   ILE B 898 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 904 through 927
      removed outlier: 3.715A  pdb=" N   ILE B 920 " --> pdb=" O   CYS B 916 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 932
      removed outlier: 3.792A  pdb=" N   ILE B 932 " --> pdb=" O   ILE B 929 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 935 through 946
      removed outlier: 3.995A  pdb=" N   LYS B 939 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL B 943 " --> pdb=" O   LYS B 939 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET B 946 " --> pdb=" O   ILE B 942 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 947 through 973
      removed outlier: 3.975A  pdb=" N   PHE B 951 " --> pdb=" O   MET B 947 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE B 953 " --> pdb=" O   ASP B 949 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   MET B 954 " --> pdb=" O   LEU B 950 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   PHE B 955 " --> pdb=" O   PHE B 951 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU B 956 " --> pdb=" O   PHE B 952 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 978 through 987
      removed outlier: 3.701A  pdb=" N   VAL B 987 " --> pdb=" O   ILE B 983 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1036 through 1065
      removed outlier: 3.789A  pdb=" N   THR B1040 " --> pdb=" O   PRO B1036 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1073 through 1092
      removed outlier: 4.199A  pdb=" N   TYR B1083 " --> pdb=" O   LYS B1079 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   GLU B1084 " --> pdb=" O   PHE B1080 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ARG B1092 " --> pdb=" O   GLU B1088 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1096 through 1114
      removed outlier: 4.262A  pdb=" N   LEU B1102 " --> pdb=" O   PRO B1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1154
    Processing helix  chain 'B' and resid 1158 through 1184
    Processing helix  chain 'B' and resid 1189 through 1208
    Processing helix  chain 'B' and resid 1270 through 1275
    Processing helix  chain 'B' and resid 1370 through 1381
    Processing helix  chain 'B' and resid 1456 through 1467
    Processing helix  chain 'C' and resid 41 through 49
      removed outlier: 3.688A  pdb=" N   ASN C  47 " --> pdb=" O   TRP C  43 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE C  48 " --> pdb=" O   ILE C  44 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 136
    Processing helix  chain 'C' and resid 159 through 177
      removed outlier: 3.608A  pdb=" N   LYS C 163 " --> pdb=" O   LYS C 159 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS C 165 " --> pdb=" O   HIS C 161 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 201
      removed outlier: 3.728A  pdb=" N   HIS C 193 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 274 through 288
    Processing helix  chain 'C' and resid 311 through 322
      removed outlier: 3.896A  pdb=" N   THR C 315 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 342
    Processing helix  chain 'C' and resid 354 through 361
    Processing helix  chain 'C' and resid 374 through 387
    Processing helix  chain 'C' and resid 406 through 419
    Processing helix  chain 'C' and resid 426 through 439
      removed outlier: 3.721A  pdb=" N   ARG C 430 " --> pdb=" O   HIS C 426 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA C 437 " --> pdb=" O   GLU C 433 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TRP C 438 " --> pdb=" O   LEU C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 440 through 448
      removed outlier: 3.849A  pdb=" N   ALA C 444 " --> pdb=" O   ARG C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 470
      removed outlier: 3.942A  pdb=" N   GLY C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 472 through 483
    Processing helix  chain 'C' and resid 485 through 490
    Processing helix  chain 'C' and resid 492 through 502
      removed outlier: 3.989A  pdb=" N   LEU C 496 " --> pdb=" O   ARG C 492 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 517
    Processing helix  chain 'C' and resid 536 through 548
    Processing helix  chain 'C' and resid 593 through 606
      removed outlier: 3.578A  pdb=" N   ASN C 606 " --> pdb=" O   ALA C 602 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 618
    Processing helix  chain 'C' and resid 620 through 639
      removed outlier: 3.893A  pdb=" N   GLU C 638 " --> pdb=" O   LYS C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 648 through 672
      removed outlier: 3.629A  pdb=" N   VAL C 664 " --> pdb=" O   GLN C 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 672 through 681
    Processing helix  chain 'C' and resid 691 through 700
    Processing helix  chain 'C' and resid 701 through 706
      removed outlier: 3.597A  pdb=" N   ILE C 705 " --> pdb=" O   ASP C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 720
    Processing helix  chain 'C' and resid 729 through 737
    Processing helix  chain 'C' and resid 738 through 743
      removed outlier: 4.066A  pdb=" N   ILE C 741 " --> pdb=" O   PHE C 738 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR C 742 " --> pdb=" O   PRO C 739 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 748 through 762
    Processing helix  chain 'C' and resid 799 through 807
    Processing helix  chain 'C' and resid 808 through 833
    Processing helix  chain 'C' and resid 840 through 865
      removed outlier: 4.008A  pdb=" N   PHE C 865 " --> pdb=" O   LEU C 861 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 870 through 880
    Processing helix  chain 'C' and resid 882 through 902
      removed outlier: 3.544A  pdb=" N   GLN C 902 " --> pdb=" O   ILE C 898 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 904 through 927
      removed outlier: 3.715A  pdb=" N   ILE C 920 " --> pdb=" O   CYS C 916 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 928 through 932
      removed outlier: 3.792A  pdb=" N   ILE C 932 " --> pdb=" O   ILE C 929 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 935 through 946
      removed outlier: 3.996A  pdb=" N   LYS C 939 " --> pdb=" O   THR C 935 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL C 943 " --> pdb=" O   LYS C 939 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET C 946 " --> pdb=" O   ILE C 942 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 947 through 973
      removed outlier: 3.975A  pdb=" N   PHE C 951 " --> pdb=" O   MET C 947 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE C 953 " --> pdb=" O   ASP C 949 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   MET C 954 " --> pdb=" O   LEU C 950 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE C 955 " --> pdb=" O   PHE C 951 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU C 956 " --> pdb=" O   PHE C 952 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 978 through 987
      removed outlier: 3.702A  pdb=" N   VAL C 987 " --> pdb=" O   ILE C 983 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1036 through 1065
      removed outlier: 3.788A  pdb=" N   THR C1040 " --> pdb=" O   PRO C1036 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1073 through 1092
      removed outlier: 4.199A  pdb=" N   TYR C1083 " --> pdb=" O   LYS C1079 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   GLU C1084 " --> pdb=" O   PHE C1080 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ARG C1092 " --> pdb=" O   GLU C1088 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1096 through 1114
      removed outlier: 4.262A  pdb=" N   LEU C1102 " --> pdb=" O   PRO C1098 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1129 through 1154
    Processing helix  chain 'C' and resid 1158 through 1184
    Processing helix  chain 'C' and resid 1189 through 1208
    Processing helix  chain 'C' and resid 1270 through 1275
    Processing helix  chain 'C' and resid 1370 through 1381
    Processing helix  chain 'C' and resid 1456 through 1467
    Processing helix  chain 'D' and resid 41 through 49
      removed outlier: 3.688A  pdb=" N   ASN D  47 " --> pdb=" O   TRP D  43 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE D  48 " --> pdb=" O   ILE D  44 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LYS D  49 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 136
    Processing helix  chain 'D' and resid 159 through 177
      removed outlier: 3.606A  pdb=" N   LYS D 163 " --> pdb=" O   LYS D 159 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS D 165 " --> pdb=" O   HIS D 161 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 201
      removed outlier: 3.728A  pdb=" N   HIS D 193 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 288
    Processing helix  chain 'D' and resid 311 through 322
      removed outlier: 3.897A  pdb=" N   THR D 315 " --> pdb=" O   GLY D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 332 through 342
    Processing helix  chain 'D' and resid 354 through 361
    Processing helix  chain 'D' and resid 374 through 387
    Processing helix  chain 'D' and resid 406 through 419
    Processing helix  chain 'D' and resid 426 through 439
      removed outlier: 3.721A  pdb=" N   ARG D 430 " --> pdb=" O   HIS D 426 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA D 437 " --> pdb=" O   GLU D 433 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TRP D 438 " --> pdb=" O   LEU D 434 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 448
      removed outlier: 3.849A  pdb=" N   ALA D 444 " --> pdb=" O   ARG D 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 460 through 470
      removed outlier: 3.943A  pdb=" N   GLY D 470 " --> pdb=" O   SER D 466 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 472 through 483
    Processing helix  chain 'D' and resid 485 through 490
    Processing helix  chain 'D' and resid 492 through 502
      removed outlier: 3.989A  pdb=" N   LEU D 496 " --> pdb=" O   ARG D 492 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 506 through 517
    Processing helix  chain 'D' and resid 536 through 548
    Processing helix  chain 'D' and resid 593 through 606
      removed outlier: 3.578A  pdb=" N   ASN D 606 " --> pdb=" O   ALA D 602 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 607 through 618
    Processing helix  chain 'D' and resid 620 through 639
      removed outlier: 3.894A  pdb=" N   GLU D 638 " --> pdb=" O   LYS D 634 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 648 through 672
      removed outlier: 3.630A  pdb=" N   VAL D 664 " --> pdb=" O   GLN D 660 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 672 through 681
    Processing helix  chain 'D' and resid 691 through 700
    Processing helix  chain 'D' and resid 701 through 706
      removed outlier: 3.596A  pdb=" N   ILE D 705 " --> pdb=" O   ASP D 701 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 707 through 720
    Processing helix  chain 'D' and resid 729 through 737
    Processing helix  chain 'D' and resid 738 through 743
      removed outlier: 4.065A  pdb=" N   ILE D 741 " --> pdb=" O   PHE D 738 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR D 742 " --> pdb=" O   PRO D 739 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 748 through 762
    Processing helix  chain 'D' and resid 799 through 807
    Processing helix  chain 'D' and resid 808 through 833
    Processing helix  chain 'D' and resid 840 through 865
      removed outlier: 4.008A  pdb=" N   PHE D 865 " --> pdb=" O   LEU D 861 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 870 through 880
    Processing helix  chain 'D' and resid 882 through 902
      removed outlier: 3.544A  pdb=" N   GLN D 902 " --> pdb=" O   ILE D 898 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 904 through 927
      removed outlier: 3.715A  pdb=" N   ILE D 920 " --> pdb=" O   CYS D 916 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 928 through 932
      removed outlier: 3.791A  pdb=" N   ILE D 932 " --> pdb=" O   ILE D 929 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 935 through 946
      removed outlier: 3.995A  pdb=" N   LYS D 939 " --> pdb=" O   THR D 935 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL D 943 " --> pdb=" O   LYS D 939 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET D 946 " --> pdb=" O   ILE D 942 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 947 through 973
      removed outlier: 3.974A  pdb=" N   PHE D 951 " --> pdb=" O   MET D 947 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE D 953 " --> pdb=" O   ASP D 949 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   MET D 954 " --> pdb=" O   LEU D 950 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE D 955 " --> pdb=" O   PHE D 951 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU D 956 " --> pdb=" O   PHE D 952 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 978 through 987
      removed outlier: 3.702A  pdb=" N   VAL D 987 " --> pdb=" O   ILE D 983 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1036 through 1065
      removed outlier: 3.789A  pdb=" N   THR D1040 " --> pdb=" O   PRO D1036 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1073 through 1092
      removed outlier: 4.199A  pdb=" N   TYR D1083 " --> pdb=" O   LYS D1079 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   GLU D1084 " --> pdb=" O   PHE D1080 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ARG D1092 " --> pdb=" O   GLU D1088 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1096 through 1114
      removed outlier: 4.262A  pdb=" N   LEU D1102 " --> pdb=" O   PRO D1098 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1129 through 1154
    Processing helix  chain 'D' and resid 1158 through 1184
    Processing helix  chain 'D' and resid 1189 through 1208
    Processing helix  chain 'D' and resid 1270 through 1275
    Processing helix  chain 'D' and resid 1370 through 1381
    Processing helix  chain 'D' and resid 1456 through 1467
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106
      removed outlier: 6.871A  pdb=" N   LYS A 117 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LEU A 262 " --> pdb=" O   LYS A 117 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA A 179 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   ILE A 215 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE A 181 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   VAL A 217 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   THR A 183 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LEU A 145 " --> pdb=" O   TRP A 180 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU A 182 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE A 147 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   GLY A 184 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   VAL A 149 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LEU A 146 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   VAL A 304 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER A 148 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   VAL A 327 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS A 303 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1361 through 1362
      removed outlier: 8.391A  pdb=" N   VAL A1411 " --> pdb=" O   TYR A1399 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   TYR A1399 " --> pdb=" O   VAL A1411 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR A1413 " --> pdb=" O   LYS A1397 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LYS A1397 " --> pdb=" O   THR A1413 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE A1415 " --> pdb=" O   VAL A1395 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1361 through 1362
      removed outlier: 6.053A  pdb=" N   PHE A1332 " --> pdb=" O   LEU A1346 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A1346 " --> pdb=" O   PHE A1332 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 106
      removed outlier: 6.871A  pdb=" N   LYS B 117 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LEU B 262 " --> pdb=" O   LYS B 117 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL B 119 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA B 179 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE B 215 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE B 181 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 217 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   THR B 183 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU B 145 " --> pdb=" O   TRP B 180 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU B 182 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE B 147 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY B 184 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   VAL B 149 " --> pdb=" O   GLY B 184 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LEU B 146 " --> pdb=" O   VAL B 302 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   VAL B 304 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER B 148 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   VAL B 327 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS B 303 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1361 through 1362
      removed outlier: 8.391A  pdb=" N   VAL B1411 " --> pdb=" O   TYR B1399 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   TYR B1399 " --> pdb=" O   VAL B1411 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   THR B1413 " --> pdb=" O   LYS B1397 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LYS B1397 " --> pdb=" O   THR B1413 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE B1415 " --> pdb=" O   VAL B1395 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1361 through 1362
      removed outlier: 6.053A  pdb=" N   PHE B1332 " --> pdb=" O   LEU B1346 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B1346 " --> pdb=" O   PHE B1332 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 106
      removed outlier: 6.871A  pdb=" N   LYS C 117 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   LEU C 262 " --> pdb=" O   LYS C 117 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL C 119 " --> pdb=" O   LEU C 262 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA C 179 " --> pdb=" O   VAL C 213 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 179 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE C 181 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL C 217 " --> pdb=" O   ILE C 181 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   THR C 183 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU C 145 " --> pdb=" O   TRP C 180 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU C 182 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE C 147 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   GLY C 184 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   VAL C 149 " --> pdb=" O   GLY C 184 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LEU C 146 " --> pdb=" O   VAL C 302 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   VAL C 304 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER C 148 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   VAL C 327 " --> pdb=" O   VAL C 301 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   CYS C 303 " --> pdb=" O   VAL C 327 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1361 through 1362
      removed outlier: 8.391A  pdb=" N   VAL C1411 " --> pdb=" O   TYR C1399 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   TYR C1399 " --> pdb=" O   VAL C1411 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR C1413 " --> pdb=" O   LYS C1397 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LYS C1397 " --> pdb=" O   THR C1413 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE C1415 " --> pdb=" O   VAL C1395 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 1361 through 1362
      removed outlier: 6.053A  pdb=" N   PHE C1332 " --> pdb=" O   LEU C1346 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU C1346 " --> pdb=" O   PHE C1332 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 104 through 106
      removed outlier: 6.872A  pdb=" N   LYS D 117 " --> pdb=" O   PHE D 260 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LEU D 262 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL D 119 " --> pdb=" O   LEU D 262 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA D 179 " --> pdb=" O   VAL D 213 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE D 215 " --> pdb=" O   ALA D 179 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ILE D 181 " --> pdb=" O   ILE D 215 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   VAL D 217 " --> pdb=" O   ILE D 181 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   THR D 183 " --> pdb=" O   VAL D 217 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU D 145 " --> pdb=" O   TRP D 180 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU D 182 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE D 147 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   GLY D 184 " --> pdb=" O   ILE D 147 " (cutoff:3.500A)
      removed outlier: 8.679A  pdb=" N   VAL D 149 " --> pdb=" O   GLY D 184 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LEU D 146 " --> pdb=" O   VAL D 302 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   VAL D 304 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER D 148 " --> pdb=" O   VAL D 304 " (cutoff:3.500A)
      removed outlier: 8.902A  pdb=" N   VAL D 327 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS D 303 " --> pdb=" O   VAL D 327 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 1361 through 1362
      removed outlier: 8.391A  pdb=" N   VAL D1411 " --> pdb=" O   TYR D1399 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   TYR D1399 " --> pdb=" O   VAL D1411 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR D1413 " --> pdb=" O   LYS D1397 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LYS D1397 " --> pdb=" O   THR D1413 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE D1415 " --> pdb=" O   VAL D1395 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 1361 through 1362
      removed outlier: 6.053A  pdb=" N   PHE D1332 " --> pdb=" O   LEU D1346 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU D1346 " --> pdb=" O   PHE D1332 " (cutoff:3.500A)

    2017 hydrogen bonds defined for protein.
    5943 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: 10.75

  Time building geometry restraints manager: 7.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 9481
        1.34 -     1.46: 5813
        1.46 -     1.58: 13462
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 28844
  Sorted by residual:
  bond pdb=" C   SER D1281 "
       pdb=" N   PRO D1282 "
    ideal  model  delta    sigma   weight residual
    1.334  1.394 -0.060 2.34e-02 1.83e+03 6.59e+00
  bond pdb=" C   SER A1281 "
       pdb=" N   PRO A1282 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.42e+00
  bond pdb=" C   SER C1281 "
       pdb=" N   PRO C1282 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.36e+00
  bond pdb=" C   SER B1281 "
       pdb=" N   PRO B1282 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.36e+00
  bond pdb=" C   PHE B 738 "
       pdb=" N   PRO B 739 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.29e+00
  ... (remaining 28839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 38632
        2.29 -     4.59: 887
        4.59 -     6.88: 105
        6.88 -     9.18: 40
        9.18 -    11.47: 8
  Bond angle restraints: 39672
  Sorted by residual:
  angle pdb=" N   PRO B 504 "
        pdb=" CA  PRO B 504 "
        pdb=" C   PRO B 504 "
      ideal   model   delta    sigma   weight residual
     112.47  123.20  -10.73 2.06e+00 2.36e-01 2.71e+01
  angle pdb=" N   PRO A 504 "
        pdb=" CA  PRO A 504 "
        pdb=" C   PRO A 504 "
      ideal   model   delta    sigma   weight residual
     112.47  123.18  -10.71 2.06e+00 2.36e-01 2.70e+01
  angle pdb=" N   PRO C 504 "
        pdb=" CA  PRO C 504 "
        pdb=" C   PRO C 504 "
      ideal   model   delta    sigma   weight residual
     112.47  123.18  -10.71 2.06e+00 2.36e-01 2.70e+01
  angle pdb=" N   PRO D 504 "
        pdb=" CA  PRO D 504 "
        pdb=" C   PRO D 504 "
      ideal   model   delta    sigma   weight residual
     112.47  123.14  -10.67 2.06e+00 2.36e-01 2.68e+01
  angle pdb=" N   SER B 505 "
        pdb=" CA  SER B 505 "
        pdb=" C   SER B 505 "
      ideal   model   delta    sigma   weight residual
     107.49  116.18   -8.69 1.74e+00 3.30e-01 2.50e+01
  ... (remaining 39667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.05: 15326
       12.05 -    24.11: 982
       24.11 -    36.16: 140
       36.16 -    48.21: 36
       48.21 -    60.27: 4
  Dihedral angle restraints: 16488
    sinusoidal: 3888
      harmonic: 12600
  Sorted by residual:
  dihedral pdb=" CA  ASP D 620 "
           pdb=" C   ASP D 620 "
           pdb=" N   CYS D 621 "
           pdb=" CA  CYS D 621 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.05  -29.95     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ASP A 620 "
           pdb=" C   ASP A 620 "
           pdb=" N   CYS A 621 "
           pdb=" CA  CYS A 621 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.06  -29.94     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  ASP C 620 "
           pdb=" C   ASP C 620 "
           pdb=" N   CYS C 621 "
           pdb=" CA  CYS C 621 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.07  -29.93     0      5.00e+00 4.00e-02 3.58e+01
  ... (remaining 16485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 4128
       0.065 -    0.130: 617
       0.130 -    0.194: 83
       0.194 -    0.259: 20
       0.259 -    0.324: 4
  Chirality restraints: 4852
  Sorted by residual:
  chirality pdb=" CA  PRO B 504 "
            pdb=" N   PRO B 504 "
            pdb=" C   PRO B 504 "
            pdb=" CB  PRO B 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO A 504 "
            pdb=" N   PRO A 504 "
            pdb=" C   PRO A 504 "
            pdb=" CB  PRO A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  PRO C 504 "
            pdb=" N   PRO C 504 "
            pdb=" C   PRO C 504 "
            pdb=" CB  PRO C 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.59e+00
  ... (remaining 4849 not shown)

  Planarity restraints: 5124
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 503 "   -0.017 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   LEU D 503 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LEU D 503 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PRO D 504 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 503 "   -0.016 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   LEU B 503 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LEU B 503 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PRO B 504 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 503 "   -0.016 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C   LEU A 503 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LEU A 503 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PRO A 504 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 5121 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 8993
        2.83 -     3.35: 26537
        3.35 -     3.86: 44867
        3.86 -     4.38: 45083
        4.38 -     4.90: 77837
  Nonbonded interactions: 203317
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D1283 "
            pdb=" OD2 ASP D1407 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR C1283 "
            pdb=" OD2 ASP C1407 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR B1283 "
            pdb=" OD2 ASP B1407 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR A1283 "
            pdb=" OD2 ASP A1407 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR B 742 "
            pdb=" O   CYS B 798 "
     model   vdw
     2.388 3.040
  ... (remaining 203312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.22
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.030
  Extract box with map and model:          1.070
  Check model and map are aligned:         0.180
  Set scattering table:                    0.240
  Process input model:                     62.480
  Find NCS groups from input model:        0.690
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.540
  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: 0.7848
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  28844  Z= 0.238
  Angle     :  0.857  11.471  39672  Z= 0.474
  Chirality :  0.050   0.324   4852
  Planarity :  0.007   0.054   5124
  Dihedral  :  8.985  60.268   8208
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.11), residues: 4060
  helix: -1.82 (0.08), residues: 2508
  sheet: -2.11 (0.25), residues: 352
  loop : -2.96 (0.15), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP C 592 
 HIS   0.011   0.002   HIS B 259 
 PHE   0.025   0.002   PHE D1280 
 TYR   0.024   0.003   TYR B1259 
 ARG   0.004   0.001   ARG B 619 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13854 ( 2009)
  hydrogen bonds       : angle       5.98280 ( 5943)
  covalent geometry    : bond        0.00495 (28844)
  covalent geometry    : angle       0.85746 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  419 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 419
  time to evaluate  : 3.170 
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  286 SER cc_start: 0.8980 (t) cc_final: 0.8757 (p)
REVERT: A  662 ILE cc_start: 0.9588 (pt) cc_final: 0.9329 (mt)
REVERT: A  679 LEU cc_start: 0.9209 (mp) cc_final: 0.8958 (tt)
REVERT: A  913 VAL cc_start: 0.8907 (t) cc_final: 0.8707 (p)
REVERT: A  922 PHE cc_start: 0.8656 (m-80) cc_final: 0.8170 (m-80)
REVERT: B  180 TRP cc_start: 0.8353 (m-10) cc_final: 0.8152 (m-10)
REVERT: B  286 SER cc_start: 0.8919 (t) cc_final: 0.8702 (p)
REVERT: B  662 ILE cc_start: 0.9632 (pt) cc_final: 0.9305 (mt)
REVERT: B  922 PHE cc_start: 0.8704 (m-80) cc_final: 0.8150 (m-80)
REVERT: C  180 TRP cc_start: 0.8357 (m-10) cc_final: 0.8153 (m-10)
REVERT: C  286 SER cc_start: 0.8919 (t) cc_final: 0.8702 (p)
REVERT: C  662 ILE cc_start: 0.9632 (pt) cc_final: 0.9300 (mt)
REVERT: C  922 PHE cc_start: 0.8707 (m-80) cc_final: 0.8157 (m-80)
REVERT: D  180 TRP cc_start: 0.8352 (m-10) cc_final: 0.8151 (m-10)
REVERT: D  286 SER cc_start: 0.8922 (t) cc_final: 0.8714 (p)
REVERT: D  662 ILE cc_start: 0.9631 (pt) cc_final: 0.9297 (mt)
REVERT: D  922 PHE cc_start: 0.8703 (m-80) cc_final: 0.8156 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 419
  average time/residue: 0.3507
  time to fit residues: 247.4454
Evaluate side-chains
  266 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 3.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 364 optimal weight:    3.9990
   chunk 327 optimal weight:   20.0000
   chunk 181 optimal weight:   30.0000
   chunk 111 optimal weight:   20.0000
   chunk 220 optimal weight:    9.9990
   chunk 174 optimal weight:   30.0000
   chunk 338 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0270
   chunk 205 optimal weight:   50.0000
   chunk 252 optimal weight:    9.9990
   chunk 392 optimal weight:    0.0370
   overall best weight:    3.2122

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

Flipped N/Q/H residues before XYZ refinement:
A 187 HIS
A 193 HIS
A 656 HIS
A 707 HIS
A1081 GLN
A1104 HIS
A1164 HIS
B 187 HIS
B 193 HIS
B 656 HIS
B 707 HIS
B1081 GLN
B1104 HIS
B1164 HIS
C 187 HIS
C 193 HIS
C 656 HIS
C 707 HIS
C1081 GLN
C1104 HIS
C1164 HIS
D 187 HIS
D 193 HIS
D 656 HIS
D 707 HIS
D1081 GLN
D1104 HIS

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.105385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084937 restraints weight = 159270.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.082148 restraints weight = 140339.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.082600 restraints weight = 128599.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  28844  Z= 0.139
  Angle     :  0.548   6.975  39672  Z= 0.293
  Chirality :  0.037   0.150   4852
  Planarity :  0.005   0.041   5124
  Dihedral  :  4.958  22.289   4412
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.77 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.13), residues: 4060
  helix:  0.49 (0.10), residues: 2556
  sheet: -1.63 (0.27), residues: 348
  loop : -2.63 (0.16), residues: 1156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 592 
 HIS   0.004   0.001   HIS A 259 
 PHE   0.014   0.001   PHE A 599 
 TYR   0.016   0.002   TYR C1259 
 ARG   0.008   0.000   ARG A1092 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 ( 2009)
  hydrogen bonds       : angle       4.03137 ( 5943)
  covalent geometry    : bond        0.00284 (28844)
  covalent geometry    : angle       0.54834 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 3.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 SER cc_start: 0.9224 (t) cc_final: 0.8971 (p)
REVERT: A  745 PHE cc_start: 0.6762 (m-80) cc_final: 0.6159 (m-80)
REVERT: A  922 PHE cc_start: 0.8458 (m-80) cc_final: 0.7795 (m-80)
REVERT: B  180 TRP cc_start: 0.8392 (m-10) cc_final: 0.8121 (m-10)
REVERT: B  286 SER cc_start: 0.9160 (t) cc_final: 0.8891 (p)
REVERT: B  922 PHE cc_start: 0.8698 (m-80) cc_final: 0.7979 (m-80)
REVERT: C  180 TRP cc_start: 0.8396 (m-10) cc_final: 0.8121 (m-10)
REVERT: C  286 SER cc_start: 0.9143 (t) cc_final: 0.8877 (p)
REVERT: C  922 PHE cc_start: 0.8690 (m-80) cc_final: 0.7968 (m-80)
REVERT: D  180 TRP cc_start: 0.8400 (m-10) cc_final: 0.8111 (m-10)
REVERT: D  286 SER cc_start: 0.9148 (t) cc_final: 0.8874 (p)
REVERT: D  922 PHE cc_start: 0.8690 (m-80) cc_final: 0.7963 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.3045
  time to fit residues: 160.2644
Evaluate side-chains
  232 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 2.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 394 optimal weight:   50.0000
   chunk 212 optimal weight:   10.0000
   chunk 204 optimal weight:    0.3980
   chunk 226 optimal weight:   10.0000
   chunk 319 optimal weight:    8.9990
   chunk 180 optimal weight:   10.0000
   chunk 304 optimal weight:   50.0000
   chunk 103 optimal weight:    7.9990
   chunk 314 optimal weight:   50.0000
   chunk 119 optimal weight:   20.0000
   chunk 389 optimal weight:    6.9990
   overall best weight:    6.8790

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

Flipped N/Q/H residues before XYZ refinement:
A 883 ASN
B 883 ASN
B1081 GLN
C 883 ASN
C1081 GLN
D 883 ASN
D1081 GLN
D1164 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.096635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.072277 restraints weight = 144500.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.069808 restraints weight = 101057.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.069735 restraints weight = 113237.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  28844  Z= 0.228
  Angle     :  0.644   9.000  39672  Z= 0.342
  Chirality :  0.040   0.155   4852
  Planarity :  0.005   0.042   5124
  Dihedral  :  4.947  22.664   4412
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.13), residues: 4060
  helix:  1.25 (0.10), residues: 2560
  sheet: -1.40 (0.29), residues: 312
  loop : -2.38 (0.17), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 592 
 HIS   0.008   0.001   HIS B 259 
 PHE   0.021   0.002   PHE A 599 
 TYR   0.020   0.002   TYR B 131 
 ARG   0.003   0.001   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 ( 2009)
  hydrogen bonds       : angle       4.20211 ( 5943)
  covalent geometry    : bond        0.00476 (28844)
  covalent geometry    : angle       0.64371 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 3.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 SER cc_start: 0.9299 (t) cc_final: 0.9044 (p)
REVERT: A  922 PHE cc_start: 0.8390 (m-80) cc_final: 0.8004 (m-80)
REVERT: B  180 TRP cc_start: 0.8459 (m-10) cc_final: 0.8164 (m-10)
REVERT: B  286 SER cc_start: 0.9244 (t) cc_final: 0.8979 (p)
REVERT: B  922 PHE cc_start: 0.8686 (m-80) cc_final: 0.7974 (m-80)
REVERT: C  180 TRP cc_start: 0.8470 (m-10) cc_final: 0.8175 (m-10)
REVERT: C  286 SER cc_start: 0.9235 (t) cc_final: 0.8976 (p)
REVERT: C  922 PHE cc_start: 0.8687 (m-80) cc_final: 0.7976 (m-80)
REVERT: C 1173 MET cc_start: 0.8234 (mmm) cc_final: 0.7980 (mmm)
REVERT: D  180 TRP cc_start: 0.8474 (m-10) cc_final: 0.8163 (m-10)
REVERT: D  286 SER cc_start: 0.9247 (t) cc_final: 0.8983 (p)
REVERT: D  922 PHE cc_start: 0.8689 (m-80) cc_final: 0.7971 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.3287
  time to fit residues: 142.1031
Evaluate side-chains
  216 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 3.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 276 optimal weight:    0.9980
   chunk 417 optimal weight:    7.9990
   chunk 269 optimal weight:    8.9990
   chunk 342 optimal weight:    8.9990
   chunk 79 optimal weight:    8.9990
   chunk 290 optimal weight:   40.0000
   chunk 418 optimal weight:    9.9990
   chunk 400 optimal weight:    9.9990
   chunk 278 optimal weight:   50.0000
   chunk 328 optimal weight:    8.9990
   chunk 219 optimal weight:    8.9990
   overall best weight:    7.1988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.072381 restraints weight = 144524.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.069723 restraints weight = 105206.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.069833 restraints weight = 109511.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  28844  Z= 0.228
  Angle     :  0.626   8.940  39672  Z= 0.332
  Chirality :  0.040   0.159   4852
  Planarity :  0.004   0.043   5124
  Dihedral  :  4.818  22.078   4412
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.13), residues: 4060
  helix:  1.37 (0.10), residues: 2584
  sheet: -1.31 (0.30), residues: 304
  loop : -2.43 (0.17), residues: 1172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.002   TRP A 592 
 HIS   0.009   0.001   HIS A 259 
 PHE   0.020   0.002   PHE A 599 
 TYR   0.019   0.002   TYR B1142 
 ARG   0.002   0.000   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 ( 2009)
  hydrogen bonds       : angle       4.17484 ( 5943)
  covalent geometry    : bond        0.00482 (28844)
  covalent geometry    : angle       0.62608 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 3.298 
Fit side-chains
REVERT: A  286 SER cc_start: 0.9283 (t) cc_final: 0.9046 (p)
REVERT: A  922 PHE cc_start: 0.8314 (m-80) cc_final: 0.7990 (m-80)
REVERT: B  180 TRP cc_start: 0.8485 (m-10) cc_final: 0.8201 (m-10)
REVERT: B  286 SER cc_start: 0.9268 (t) cc_final: 0.9001 (p)
REVERT: B  922 PHE cc_start: 0.8605 (m-80) cc_final: 0.8134 (m-80)
REVERT: B 1173 MET cc_start: 0.8368 (mmm) cc_final: 0.8099 (mmm)
REVERT: C  180 TRP cc_start: 0.8507 (m-10) cc_final: 0.8224 (m-10)
REVERT: C  286 SER cc_start: 0.9277 (t) cc_final: 0.9011 (p)
REVERT: C  922 PHE cc_start: 0.8608 (m-80) cc_final: 0.8139 (m-80)
REVERT: D  180 TRP cc_start: 0.8501 (m-10) cc_final: 0.8210 (m-10)
REVERT: D  286 SER cc_start: 0.9268 (t) cc_final: 0.9003 (p)
REVERT: D  922 PHE cc_start: 0.8620 (m-80) cc_final: 0.8171 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.3441
  time to fit residues: 145.3212
Evaluate side-chains
  205 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 3.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 274 optimal weight:    7.9990
   chunk 206 optimal weight:   50.0000
   chunk 301 optimal weight:    1.9990
   chunk 162 optimal weight:   30.0000
   chunk 130 optimal weight:    8.9990
   chunk 89 optimal weight:   50.0000
   chunk 220 optimal weight:    9.9990
   chunk 99 optimal weight:   40.0000
   chunk 106 optimal weight:    8.9990
   chunk 404 optimal weight:    0.0040
   chunk 16 optimal weight:    9.9990
   overall best weight:    5.6000

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.102034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.080573 restraints weight = 159498.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.078176 restraints weight = 125797.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.078437 restraints weight = 131974.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  28844  Z= 0.181
  Angle     :  0.573   7.756  39672  Z= 0.301
  Chirality :  0.038   0.154   4852
  Planarity :  0.004   0.037   5124
  Dihedral  :  4.565  22.597   4412
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.13), residues: 4060
  helix:  1.67 (0.10), residues: 2580
  sheet: -1.03 (0.32), residues: 284
  loop : -2.38 (0.17), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP D 592 
 HIS   0.007   0.001   HIS A 259 
 PHE   0.014   0.002   PHE C1280 
 TYR   0.014   0.002   TYR A 500 
 ARG   0.003   0.000   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03549 ( 2009)
  hydrogen bonds       : angle       3.92217 ( 5943)
  covalent geometry    : bond        0.00383 (28844)
  covalent geometry    : angle       0.57334 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 3.211 
Fit side-chains
REVERT: A  286 SER cc_start: 0.9296 (t) cc_final: 0.9023 (p)
REVERT: A  922 PHE cc_start: 0.8351 (m-80) cc_final: 0.8012 (m-80)
REVERT: A 1140 GLU cc_start: 0.8707 (pp20) cc_final: 0.8280 (pp20)
REVERT: B  180 TRP cc_start: 0.8492 (m-10) cc_final: 0.8232 (m-10)
REVERT: B  286 SER cc_start: 0.9287 (t) cc_final: 0.9028 (p)
REVERT: B  922 PHE cc_start: 0.8577 (m-80) cc_final: 0.8124 (m-80)
REVERT: B 1173 MET cc_start: 0.8331 (mmm) cc_final: 0.7982 (mmm)
REVERT: C  180 TRP cc_start: 0.8516 (m-10) cc_final: 0.8247 (m-10)
REVERT: C  286 SER cc_start: 0.9288 (t) cc_final: 0.9025 (p)
REVERT: C  922 PHE cc_start: 0.8576 (m-80) cc_final: 0.8095 (m-80)
REVERT: C 1173 MET cc_start: 0.8205 (mmm) cc_final: 0.7941 (mmp)
REVERT: D  180 TRP cc_start: 0.8495 (m-10) cc_final: 0.8227 (m-10)
REVERT: D  286 SER cc_start: 0.9289 (t) cc_final: 0.9028 (p)
REVERT: D  922 PHE cc_start: 0.8571 (m-80) cc_final: 0.8100 (m-80)
REVERT: D 1173 MET cc_start: 0.8331 (mmm) cc_final: 0.7901 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2922
  time to fit residues: 130.2466
Evaluate side-chains
  218 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 3.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 73 optimal weight:   40.0000
   chunk 68 optimal weight:   30.0000
   chunk 250 optimal weight:    3.9990
   chunk 255 optimal weight:    6.9990
   chunk 213 optimal weight:   50.0000
   chunk 315 optimal weight:   50.0000
   chunk 390 optimal weight:   30.0000
   chunk 372 optimal weight:    3.9990
   chunk 396 optimal weight:    0.7980
   chunk 383 optimal weight:   20.0000
   chunk 240 optimal weight:    1.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.103935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.082987 restraints weight = 157113.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.080371 restraints weight = 141459.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.080661 restraints weight = 155008.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  28844  Z= 0.130
  Angle     :  0.509   6.842  39672  Z= 0.267
  Chirality :  0.037   0.148   4852
  Planarity :  0.004   0.067   5124
  Dihedral  :  4.272  23.119   4412
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.14), residues: 4060
  helix:  1.97 (0.10), residues: 2588
  sheet: -0.99 (0.30), residues: 292
  loop : -2.36 (0.17), residues: 1180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP D 592 
 HIS   0.005   0.001   HIS C 259 
 PHE   0.013   0.001   PHE B1280 
 TYR   0.014   0.001   TYR B1259 
 ARG   0.003   0.000   ARG B 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 ( 2009)
  hydrogen bonds       : angle       3.58295 ( 5943)
  covalent geometry    : bond        0.00275 (28844)
  covalent geometry    : angle       0.50851 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 3.131 
Fit side-chains
REVERT: A  802 LEU cc_start: 0.9321 (tt) cc_final: 0.9081 (mm)
REVERT: A  922 PHE cc_start: 0.8455 (m-80) cc_final: 0.8009 (m-10)
REVERT: A 1140 GLU cc_start: 0.8522 (pp20) cc_final: 0.8256 (tm-30)
REVERT: B  286 SER cc_start: 0.9104 (t) cc_final: 0.8883 (p)
REVERT: B  802 LEU cc_start: 0.9282 (tt) cc_final: 0.9062 (mm)
REVERT: B  922 PHE cc_start: 0.8655 (m-80) cc_final: 0.8024 (m-80)
REVERT: B 1173 MET cc_start: 0.8169 (mmm) cc_final: 0.7966 (mmm)
REVERT: C  286 SER cc_start: 0.9077 (t) cc_final: 0.8873 (p)
REVERT: C  802 LEU cc_start: 0.9261 (tt) cc_final: 0.9045 (mm)
REVERT: C  922 PHE cc_start: 0.8644 (m-80) cc_final: 0.7967 (m-80)
REVERT: D  286 SER cc_start: 0.9095 (t) cc_final: 0.8862 (p)
REVERT: D  802 LEU cc_start: 0.9302 (tt) cc_final: 0.9080 (mm)
REVERT: D  922 PHE cc_start: 0.8647 (m-80) cc_final: 0.7988 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2924
  time to fit residues: 129.9834
Evaluate side-chains
  219 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 3.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 238 optimal weight:    8.9990
   chunk 97 optimal weight:   50.0000
   chunk 406 optimal weight:    4.9990
   chunk 282 optimal weight:   20.0000
   chunk 204 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 90 optimal weight:    0.4980
   chunk 178 optimal weight:   10.0000
   chunk 179 optimal weight:    8.9990
   chunk 70 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   overall best weight:    6.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 538 HIS
B 538 HIS
C 538 HIS
D 538 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.101795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.080969 restraints weight = 155641.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.077857 restraints weight = 129473.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.078041 restraints weight = 122021.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  28844  Z= 0.213
  Angle     :  0.610   8.879  39672  Z= 0.320
  Chirality :  0.039   0.208   4852
  Planarity :  0.004   0.051   5124
  Dihedral  :  4.564  22.518   4412
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.14), residues: 4060
  helix:  1.83 (0.10), residues: 2588
  sheet: -1.12 (0.31), residues: 284
  loop : -2.30 (0.17), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 592 
 HIS   0.008   0.001   HIS A 259 
 PHE   0.015   0.002   PHE A 665 
 TYR   0.015   0.002   TYR C 131 
 ARG   0.003   0.000   ARG B1152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 ( 2009)
  hydrogen bonds       : angle       4.01495 ( 5943)
  covalent geometry    : bond        0.00449 (28844)
  covalent geometry    : angle       0.61011 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 3.274 
Fit side-chains
REVERT: A  802 LEU cc_start: 0.9453 (tt) cc_final: 0.9177 (mm)
REVERT: A  922 PHE cc_start: 0.8464 (m-80) cc_final: 0.8114 (m-80)
REVERT: A 1140 GLU cc_start: 0.8651 (pp20) cc_final: 0.8259 (pp20)
REVERT: B  802 LEU cc_start: 0.9396 (tt) cc_final: 0.9123 (mm)
REVERT: B  922 PHE cc_start: 0.8739 (m-80) cc_final: 0.8008 (m-80)
REVERT: B 1173 MET cc_start: 0.8071 (mmm) cc_final: 0.7825 (mmm)
REVERT: C  802 LEU cc_start: 0.9408 (tt) cc_final: 0.9136 (mm)
REVERT: C  922 PHE cc_start: 0.8608 (m-80) cc_final: 0.8191 (m-80)
REVERT: D  802 LEU cc_start: 0.9421 (tt) cc_final: 0.9151 (mm)
REVERT: D  922 PHE cc_start: 0.8735 (m-80) cc_final: 0.7998 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2926
  time to fit residues: 124.2491
Evaluate side-chains
  192 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 3.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 104 optimal weight:   50.0000
   chunk 287 optimal weight:   30.0000
   chunk 191 optimal weight:    5.9990
   chunk 319 optimal weight:   30.0000
   chunk 429 optimal weight:   40.0000
   chunk 300 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 312 optimal weight:    8.9990
   chunk 397 optimal weight:   30.0000
   chunk 341 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.102704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.081816 restraints weight = 155759.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.078905 restraints weight = 125864.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.078989 restraints weight = 128927.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  28844  Z= 0.172
  Angle     :  0.559   7.401  39672  Z= 0.294
  Chirality :  0.038   0.162   4852
  Planarity :  0.004   0.047   5124
  Dihedral  :  4.431  22.660   4412
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.14), residues: 4060
  helix:  1.94 (0.10), residues: 2584
  sheet: -1.20 (0.30), residues: 284
  loop : -2.27 (0.17), residues: 1192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP B 592 
 HIS   0.007   0.001   HIS A 259 
 PHE   0.012   0.002   PHE D 665 
 TYR   0.013   0.001   TYR C1142 
 ARG   0.002   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 ( 2009)
  hydrogen bonds       : angle       3.80883 ( 5943)
  covalent geometry    : bond        0.00363 (28844)
  covalent geometry    : angle       0.55864 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 3.433 
Fit side-chains
REVERT: A  802 LEU cc_start: 0.9491 (tt) cc_final: 0.9199 (mm)
REVERT: A  922 PHE cc_start: 0.8482 (m-80) cc_final: 0.8103 (m-80)
REVERT: A 1140 GLU cc_start: 0.8700 (pp20) cc_final: 0.8390 (pp20)
REVERT: B  802 LEU cc_start: 0.9443 (tt) cc_final: 0.9173 (mm)
REVERT: B  922 PHE cc_start: 0.8718 (m-80) cc_final: 0.8004 (m-80)
REVERT: B 1173 MET cc_start: 0.8705 (mmm) cc_final: 0.8217 (mmm)
REVERT: C  802 LEU cc_start: 0.9455 (tt) cc_final: 0.9183 (mm)
REVERT: C  922 PHE cc_start: 0.8718 (m-80) cc_final: 0.8012 (m-80)
REVERT: C 1173 MET cc_start: 0.8722 (mmm) cc_final: 0.8393 (mmp)
REVERT: D  802 LEU cc_start: 0.9467 (tt) cc_final: 0.9198 (mm)
REVERT: D  922 PHE cc_start: 0.8720 (m-80) cc_final: 0.7993 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2964
  time to fit residues: 124.4530
Evaluate side-chains
  198 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 3.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 195 optimal weight:    8.9990
   chunk 403 optimal weight:    0.7980
   chunk 326 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 297 optimal weight:    8.9990
   chunk 266 optimal weight:    7.9990
   chunk 353 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 264 optimal weight:    3.9990
   chunk 283 optimal weight:    8.9990
   chunk 261 optimal weight:    9.9990
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.102584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.082009 restraints weight = 155425.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.078943 restraints weight = 135830.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.079211 restraints weight = 151030.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  28844  Z= 0.177
  Angle     :  0.568   7.662  39672  Z= 0.298
  Chirality :  0.038   0.201   4852
  Planarity :  0.004   0.043   5124
  Dihedral  :  4.429  23.098   4412
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.14), residues: 4060
  helix:  1.96 (0.10), residues: 2592
  sheet: -1.17 (0.29), residues: 292
  loop : -2.25 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP C 592 
 HIS   0.007   0.001   HIS C 259 
 PHE   0.012   0.002   PHE C 665 
 TYR   0.015   0.002   TYR B1089 
 ARG   0.002   0.000   ARG D1152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 ( 2009)
  hydrogen bonds       : angle       3.82149 ( 5943)
  covalent geometry    : bond        0.00375 (28844)
  covalent geometry    : angle       0.56758 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 3.469 
Fit side-chains
REVERT: A  802 LEU cc_start: 0.9439 (tt) cc_final: 0.9157 (mm)
REVERT: A  922 PHE cc_start: 0.8505 (m-80) cc_final: 0.8088 (m-80)
REVERT: A 1140 GLU cc_start: 0.8659 (pp20) cc_final: 0.8166 (pp20)
REVERT: B  802 LEU cc_start: 0.9389 (tt) cc_final: 0.9130 (mm)
REVERT: B  922 PHE cc_start: 0.8753 (m-80) cc_final: 0.7965 (m-80)
REVERT: B 1140 GLU cc_start: 0.8696 (pp20) cc_final: 0.8251 (pp20)
REVERT: C  802 LEU cc_start: 0.9397 (tt) cc_final: 0.9137 (mm)
REVERT: C  922 PHE cc_start: 0.8728 (m-80) cc_final: 0.7959 (m-80)
REVERT: C 1140 GLU cc_start: 0.8658 (pp20) cc_final: 0.8182 (pp20)
REVERT: D  802 LEU cc_start: 0.9416 (tt) cc_final: 0.9155 (mm)
REVERT: D  922 PHE cc_start: 0.8740 (m-80) cc_final: 0.7950 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.3001
  time to fit residues: 125.2992
Evaluate side-chains
  198 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 3.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 225 optimal weight:   20.0000
   chunk 144 optimal weight:   20.0000
   chunk 250 optimal weight:    6.9990
   chunk 398 optimal weight:   30.0000
   chunk 354 optimal weight:    4.9990
   chunk 329 optimal weight:    4.9990
   chunk 306 optimal weight:    0.0010
   chunk 321 optimal weight:   50.0000
   chunk 185 optimal weight:    5.9990
   chunk 211 optimal weight:   50.0000
   overall best weight:    4.5994

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.103257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.083287 restraints weight = 155967.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.080689 restraints weight = 141500.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.081276 restraints weight = 119602.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  28844  Z= 0.156
  Angle     :  0.544   7.770  39672  Z= 0.285
  Chirality :  0.038   0.169   4852
  Planarity :  0.004   0.043   5124
  Dihedral  :  4.326  22.785   4412
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.14), residues: 4060
  helix:  2.02 (0.10), residues: 2612
  sheet: -1.38 (0.28), residues: 312
  loop : -2.26 (0.17), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 592 
 HIS   0.005   0.001   HIS D 259 
 PHE   0.010   0.001   PHE B1280 
 TYR   0.015   0.001   TYR A1089 
 ARG   0.002   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 ( 2009)
  hydrogen bonds       : angle       3.70866 ( 5943)
  covalent geometry    : bond        0.00331 (28844)
  covalent geometry    : angle       0.54436 (39672)

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

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

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8120 Ramachandran restraints generated.
    4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 3.056 
Fit side-chains
REVERT: A  922 PHE cc_start: 0.8483 (m-80) cc_final: 0.8020 (m-80)
REVERT: A 1140 GLU cc_start: 0.8706 (pp20) cc_final: 0.8248 (pp20)
REVERT: B  922 PHE cc_start: 0.8739 (m-80) cc_final: 0.7945 (m-80)
REVERT: B 1140 GLU cc_start: 0.8680 (pp20) cc_final: 0.8342 (pp20)
REVERT: C  922 PHE cc_start: 0.8709 (m-80) cc_final: 0.7943 (m-80)
REVERT: C 1140 GLU cc_start: 0.8780 (pp20) cc_final: 0.8476 (pp20)
REVERT: D  922 PHE cc_start: 0.8724 (m-80) cc_final: 0.7945 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.3031
  time to fit residues: 131.0435
Evaluate side-chains
  209 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 3.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 432
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 307 optimal weight:    8.9990
   chunk 140 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 386 optimal weight:    0.9990
   chunk 188 optimal weight:    4.9990
   chunk 381 optimal weight:    5.9990
   chunk 311 optimal weight:   30.0000
   chunk 370 optimal weight:    0.8980
   chunk 392 optimal weight:    6.9990
   chunk 379 optimal weight:   30.0000
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.104787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.084924 restraints weight = 155979.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.082478 restraints weight = 148536.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.082888 restraints weight = 145640.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  28844  Z= 0.112
  Angle     :  0.503   6.952  39672  Z= 0.259
  Chirality :  0.037   0.146   4852
  Planarity :  0.004   0.042   5124
  Dihedral  :  4.093  23.340   4412
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.14), residues: 4060
  helix:  2.27 (0.10), residues: 2584
  sheet: -1.27 (0.28), residues: 312
  loop : -2.22 (0.17), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP B 592 
 HIS   0.003   0.001   HIS C 259 
 PHE   0.010   0.001   PHE C 665 
 TYR   0.013   0.001   TYR C1259 
 ARG   0.003   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 ( 2009)
  hydrogen bonds       : angle       3.42735 ( 5943)
  covalent geometry    : bond        0.00238 (28844)
  covalent geometry    : angle       0.50283 (39672)

===============================================================================
Job complete
usr+sys time: 8064.68 seconds
wall clock time: 140 minutes 7.02 seconds (8407.02 seconds total)