Starting phenix.real_space_refine
on Wed May 15 13:09:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1c_18807/05_2024/8r1c_18807.pdb"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.081
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     141      5.16       5
     C   19377      2.51       5
     N    5010      2.21       5
     O    5898      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   50": "OD1" <-> "OD2"
    Residue "A PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  306": "OE1" <-> "OE2"
    Residue "A PHE  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  372": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  386": "OD1" <-> "OD2"
    Residue "A PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  575": "OD1" <-> "OD2"
    Residue "A GLU  658": "OE1" <-> "OE2"
    Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   27": "OD1" <-> "OD2"
    Residue "E TYR   38": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   84": "OD1" <-> "OD2"
    Residue "E TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  101": "OD1" <-> "OD2"
    Residue "B ASP   50": "OD1" <-> "OD2"
    Residue "B PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  306": "OE1" <-> "OE2"
    Residue "B PHE  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  372": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  386": "OD1" <-> "OD2"
    Residue "B PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  575": "OD1" <-> "OD2"
    Residue "B GLU  658": "OE1" <-> "OE2"
    Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   50": "OD1" <-> "OD2"
    Residue "C PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  306": "OE1" <-> "OE2"
    Residue "C PHE  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  372": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  386": "OD1" <-> "OD2"
    Residue "C PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  575": "OD1" <-> "OD2"
    Residue "C GLU  658": "OE1" <-> "OE2"
    Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 30426
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 8276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1056, 8276
          Classifications: {'peptide': 1056}
          Link IDs: {'PTRANS': 51, 'TRANS': 1004}
          Chain breaks: 6
    Chain: "H"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 931
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 795
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 931
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "E"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 795
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "F"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 931
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "G"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 795
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "B"
      Number of atoms: 8276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1056, 8276
          Classifications: {'peptide': 1056}
          Link IDs: {'PTRANS': 51, 'TRANS': 1004}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 8276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1056, 8276
          Classifications: {'peptide': 1056}
          Link IDs: {'PTRANS': 51, 'TRANS': 1004}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "B"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "C"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 15.63, per 1000 atoms: 0.51
  Number of scatterers: 30426
  At special positions: 0
  Unit cell: (159.936, 152.633, 171.62, 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     141     16.00
     O    5898      8.00
     N    5010      7.00
     C   19377      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=51, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 535 " - pdb=" SG  CYS A 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 614 " - pdb=" SG  CYS A 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 659 " - pdb=" SG  CYS A 668 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 735 " - pdb=" SG  CYS A 757 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 740 " - pdb=" SG  CYS A 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1029 " - pdb=" SG  CYS A1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1079 " - pdb=" SG  CYS A1123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 103 " - pdb=" SG  CYS H 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 103 " - pdb=" SG  CYS F 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 535 " - pdb=" SG  CYS B 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 646 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 659 " - pdb=" SG  CYS B 668 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 735 " - pdb=" SG  CYS B 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 740 " - pdb=" SG  CYS B 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 837 " - pdb=" SG  CYS B 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1029 " - pdb=" SG  CYS B1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1079 " - pdb=" SG  CYS B1123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 288 " - pdb=" SG  CYS C 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 333 " - pdb=" SG  CYS C 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 376 " - pdb=" SG  CYS C 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 388 " - pdb=" SG  CYS C 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 477 " - pdb=" SG  CYS C 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 535 " - pdb=" SG  CYS C 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 614 " - pdb=" SG  CYS C 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 659 " - pdb=" SG  CYS C 668 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 735 " - pdb=" SG  CYS C 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 740 " - pdb=" SG  CYS C 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 837 " - pdb=" SG  CYS C 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1029 " - pdb=" SG  CYS C1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1079 " - pdb=" SG  CYS C1123 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 654 "
      " NAG A1302 " - " ASN A 714 "
      " NAG A1303 " - " ASN A 798 "
      " NAG A1304 " - " ASN A1131 "
      " NAG A1305 " - " ASN A 706 "
      " NAG A1306 " - " ASN A 613 "
      " NAG A1307 " - " ASN A1095 "
      " NAG A1308 " - " ASN A 279 "
      " NAG A1309 " - " ASN A1071 "
      " NAG A1310 " - " ASN A 231 "
      " NAG B1301 " - " ASN B 654 "
      " NAG B1302 " - " ASN B 714 "
      " NAG B1303 " - " ASN B 798 "
      " NAG B1304 " - " ASN B1131 "
      " NAG B1305 " - " ASN B 706 "
      " NAG B1306 " - " ASN B 613 "
      " NAG B1307 " - " ASN B1095 "
      " NAG B1308 " - " ASN B 279 "
      " NAG B1309 " - " ASN B1071 "
      " NAG B1310 " - " ASN B 231 "
      " NAG C1301 " - " ASN C 654 "
      " NAG C1302 " - " ASN C 714 "
      " NAG C1303 " - " ASN C 798 "
      " NAG C1304 " - " ASN C1131 "
      " NAG C1305 " - " ASN C 706 "
      " NAG C1306 " - " ASN C 613 "
      " NAG C1307 " - " ASN C1095 "
      " NAG C1308 " - " ASN C 279 "
      " NAG C1309 " - " ASN C1071 "
      " NAG C1310 " - " ASN C 231 "
  Time building additional restraints: 12.03
  Conformation dependent library (CDL) restraints added in 7.0 seconds
  

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7194

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 69 sheets defined
      22.9% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 291 through 301
    Processing helix  chain 'A' and resid 334 through 340
      removed outlier: 3.750A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 368
      removed outlier: 3.759A  pdb=" N   VAL A 364 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR A 366 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 386
      removed outlier: 4.526A  pdb=" N   ASN A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
      removed outlier: 4.669A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 419
    Processing helix  chain 'A' and resid 435 through 440
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 613 through 617
    Processing helix  chain 'A' and resid 734 through 741
    Processing helix  chain 'A' and resid 743 through 751
    Processing helix  chain 'A' and resid 752 through 754
      No H-bonds generated for 'chain 'A' and resid 752 through 754'
    Processing helix  chain 'A' and resid 755 through 780
      removed outlier: 3.649A  pdb=" N   ASP A 772 " --> pdb=" O   ALA A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 845 through 853
      removed outlier: 3.893A  pdb=" N   ALA A 849 " --> pdb=" O   ASP A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 882
    Processing helix  chain 'A' and resid 883 through 888
      removed outlier: 3.820A  pdb=" N   ALA A 887 " --> pdb=" O   TRP A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 906
    Processing helix  chain 'A' and resid 909 through 916
      removed outlier: 3.951A  pdb=" N   LEU A 913 " --> pdb=" O   THR A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 938
    Processing helix  chain 'A' and resid 942 through 962
    Processing helix  chain 'A' and resid 963 through 965
      No H-bonds generated for 'chain 'A' and resid 963 through 965'
    Processing helix  chain 'A' and resid 973 through 981
    Processing helix  chain 'A' and resid 982 through 1030
    Processing helix  chain 'A' and resid 1137 through 1144
      removed outlier: 4.033A  pdb=" N   GLU A1141 " --> pdb=" O   PRO A1137 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 63 through 66
      removed outlier: 3.505A  pdb=" N   LYS D  66 " --> pdb=" O   PRO D  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 63 through 66'
    Processing helix  chain 'F' and resid 28 through 32
    Processing helix  chain 'F' and resid 63 through 66
      removed outlier: 3.509A  pdb=" N   LYS F  66 " --> pdb=" O   PRO F  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 63 through 66'
    Processing helix  chain 'B' and resid 291 through 301
    Processing helix  chain 'B' and resid 334 through 340
      removed outlier: 3.750A  pdb=" N   VAL B 338 " --> pdb=" O   PRO B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 368
      removed outlier: 3.759A  pdb=" N   VAL B 364 " --> pdb=" O   ASP B 361 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR B 366 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 386
      removed outlier: 4.526A  pdb=" N   ASN B 385 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 407
      removed outlier: 4.669A  pdb=" N   SER B 405 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 435 through 440
    Processing helix  chain 'B' and resid 499 through 502
    Processing helix  chain 'B' and resid 613 through 617
    Processing helix  chain 'B' and resid 734 through 741
    Processing helix  chain 'B' and resid 743 through 751
    Processing helix  chain 'B' and resid 752 through 754
      No H-bonds generated for 'chain 'B' and resid 752 through 754'
    Processing helix  chain 'B' and resid 755 through 780
      removed outlier: 3.649A  pdb=" N   ASP B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 823
    Processing helix  chain 'B' and resid 845 through 853
      removed outlier: 3.893A  pdb=" N   ALA B 849 " --> pdb=" O   ASP B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 863 through 882
    Processing helix  chain 'B' and resid 883 through 888
      removed outlier: 3.820A  pdb=" N   ALA B 887 " --> pdb=" O   TRP B 883 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 906
    Processing helix  chain 'B' and resid 909 through 916
      removed outlier: 3.952A  pdb=" N   LEU B 913 " --> pdb=" O   THR B 909 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 916 through 938
    Processing helix  chain 'B' and resid 942 through 962
    Processing helix  chain 'B' and resid 963 through 965
      No H-bonds generated for 'chain 'B' and resid 963 through 965'
    Processing helix  chain 'B' and resid 973 through 981
    Processing helix  chain 'B' and resid 982 through 1030
    Processing helix  chain 'B' and resid 1137 through 1144
      removed outlier: 4.034A  pdb=" N   GLU B1141 " --> pdb=" O   PRO B1137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 301
    Processing helix  chain 'C' and resid 334 through 340
      removed outlier: 3.750A  pdb=" N   VAL C 338 " --> pdb=" O   PRO C 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 368
      removed outlier: 3.759A  pdb=" N   VAL C 364 " --> pdb=" O   ASP C 361 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR C 366 " --> pdb=" O   SER C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 386
      removed outlier: 4.526A  pdb=" N   ASN C 385 " --> pdb=" O   THR C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 407
      removed outlier: 4.669A  pdb=" N   SER C 405 " --> pdb=" O   ASN C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 419
    Processing helix  chain 'C' and resid 435 through 440
    Processing helix  chain 'C' and resid 499 through 502
    Processing helix  chain 'C' and resid 613 through 617
    Processing helix  chain 'C' and resid 734 through 741
    Processing helix  chain 'C' and resid 743 through 751
    Processing helix  chain 'C' and resid 752 through 754
      No H-bonds generated for 'chain 'C' and resid 752 through 754'
    Processing helix  chain 'C' and resid 755 through 780
      removed outlier: 3.650A  pdb=" N   ASP C 772 " --> pdb=" O   ALA C 768 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 813 through 823
    Processing helix  chain 'C' and resid 845 through 853
      removed outlier: 3.893A  pdb=" N   ALA C 849 " --> pdb=" O   ASP C 845 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 863 through 882
    Processing helix  chain 'C' and resid 883 through 888
      removed outlier: 3.820A  pdb=" N   ALA C 887 " --> pdb=" O   TRP C 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 906
    Processing helix  chain 'C' and resid 909 through 916
      removed outlier: 3.952A  pdb=" N   LEU C 913 " --> pdb=" O   THR C 909 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 916 through 938
    Processing helix  chain 'C' and resid 942 through 962
    Processing helix  chain 'C' and resid 963 through 965
      No H-bonds generated for 'chain 'C' and resid 963 through 965'
    Processing helix  chain 'C' and resid 973 through 981
    Processing helix  chain 'C' and resid 982 through 1030
    Processing helix  chain 'C' and resid 1137 through 1144
      removed outlier: 4.033A  pdb=" N   GLU C1141 " --> pdb=" O   PRO C1137 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27
      removed outlier: 7.666A  pdb=" N   ASN A  58 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   TYR A 266 " --> pdb=" O   ASN A  58 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   SER A 202 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52
      removed outlier: 3.866A  pdb=" N   ASP A 284 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132
      removed outlier: 5.949A  pdb=" N   GLU A 129 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ALA A 160 " --> pdb=" O   GLU A 129 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLN A 131 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 140
      removed outlier: 3.990A  pdb=" N   ASP A 139 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316
      removed outlier: 4.397A  pdb=" N   VAL A 592 " --> pdb=" O   THR A 312 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   ASN A 314 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLY A 590 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   GLY A 591 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325
      removed outlier: 4.204A  pdb=" N   GLU A 321 " --> pdb=" O   CYS A 535 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   ASP A 571 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355
    Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359
      removed outlier: 6.567A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652
      removed outlier: 6.145A  pdb=" N   ALA A 669 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701
      removed outlier: 6.460A  pdb=" N   ASN A 700 " --> pdb=" O   LYS B 787 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712
      removed outlier: 3.857A  pdb=" N   ALA A1075 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   PHE A1092 " --> pdb=" O   ALA A1075 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725
      removed outlier: 5.904A  pdb=" N   TYR A1064 " --> pdb=" O   HIS A1045 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   HIS A1045 " --> pdb=" O   TYR A1064 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733
      removed outlier: 4.464A  pdb=" N   LYS A 730 " --> pdb=" O   LEU A 858 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119
    Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.231A  pdb=" N   TRP H  36 " --> pdb=" O   ARG H  52 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG H  52 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP H  38 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.988A  pdb=" N   ILE H 113 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP H 101 " --> pdb=" O   PHE H 111 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   PHE H 111 " --> pdb=" O   ASP H 101 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.411A  pdb=" N   TRP L  37 " --> pdb=" O   MET L  49 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12
      removed outlier: 5.877A  pdb=" N   THR L  98 " --> pdb=" O   ALA L  94 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.595A  pdb=" N   GLY D  51 " --> pdb=" O   TRP D  38 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ARG D  40 " --> pdb=" O   TRP D  49 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   TRP D  49 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.996A  pdb=" N   ILE D 113 " --> pdb=" O   ARG D  99 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ASP D 101 " --> pdb=" O   PHE D 111 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   PHE D 111 " --> pdb=" O   ASP D 101 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12
      removed outlier: 6.416A  pdb=" N   TRP E  37 " --> pdb=" O   MET E  49 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12
      removed outlier: 5.914A  pdb=" N   THR E  98 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 18 through 23
    Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   GLY F  51 " --> pdb=" O   TRP F  38 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG F  40 " --> pdb=" O   TRP F  49 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   TRP F  49 " --> pdb=" O   ARG F  40 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'F' and resid 11 through 12
      removed outlier: 4.001A  pdb=" N   ILE F 113 " --> pdb=" O   ARG F  99 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ASP F 101 " --> pdb=" O   PHE F 111 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   PHE F 111 " --> pdb=" O   ASP F 101 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 12
      removed outlier: 6.436A  pdb=" N   TRP G  37 " --> pdb=" O   MET G  49 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 12
      removed outlier: 5.894A  pdb=" N   THR G  98 " --> pdb=" O   ALA G  94 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'G' and resid 18 through 23
    Processing sheet with id=AE1, first strand: chain 'B' and resid 23 through 27
      removed outlier: 7.666A  pdb=" N   ASN B  58 " --> pdb=" O   TYR B 266 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   TYR B 266 " --> pdb=" O   ASN B  58 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   SER B 202 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'B' and resid 44 through 52
      removed outlier: 3.866A  pdb=" N   ASP B 284 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'B' and resid 81 through 82
    Processing sheet with id=AE4, first strand: chain 'B' and resid 129 through 132
      removed outlier: 5.950A  pdb=" N   GLU B 129 " --> pdb=" O   ALA B 160 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ALA B 160 " --> pdb=" O   GLU B 129 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLN B 131 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'B' and resid 139 through 140
      removed outlier: 3.990A  pdb=" N   ASP B 139 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'B' and resid 308 through 316
      removed outlier: 4.397A  pdb=" N   VAL B 592 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASN B 314 " --> pdb=" O   GLY B 590 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   GLY B 590 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY B 591 " --> pdb=" O   GLN B 610 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'B' and resid 321 through 325
      removed outlier: 4.203A  pdb=" N   GLU B 321 " --> pdb=" O   CYS B 535 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   ASP B 571 " --> pdb=" O   ILE B 584 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'B' and resid 351 through 355
    Processing sheet with id=AE9, first strand: chain 'B' and resid 358 through 359
      removed outlier: 6.567A  pdb=" N   CYS B 358 " --> pdb=" O   CYS B 522 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AF2, first strand: chain 'B' and resid 470 through 471
    Processing sheet with id=AF3, first strand: chain 'B' and resid 651 through 652
      removed outlier: 6.145A  pdb=" N   ALA B 669 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'B' and resid 699 through 701
      removed outlier: 6.460A  pdb=" N   ASN B 700 " --> pdb=" O   LYS C 787 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF4
    Processing sheet with id=AF5, first strand: chain 'B' and resid 708 through 712
      removed outlier: 3.856A  pdb=" N   ALA B1075 " --> pdb=" O   PHE B1092 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   PHE B1092 " --> pdb=" O   ALA B1075 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'B' and resid 715 through 725
      removed outlier: 5.903A  pdb=" N   TYR B1064 " --> pdb=" O   HIS B1045 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   HIS B1045 " --> pdb=" O   TYR B1064 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'B' and resid 730 through 733
      removed outlier: 4.464A  pdb=" N   LYS B 730 " --> pdb=" O   LEU B 858 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'B' and resid 1117 through 1119
    Processing sheet with id=AF9, first strand: chain 'C' and resid 23 through 27
      removed outlier: 7.666A  pdb=" N   ASN C  58 " --> pdb=" O   TYR C 266 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   TYR C 266 " --> pdb=" O   ASN C  58 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER C 202 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
    Processing sheet with id=AG1, first strand: chain 'C' and resid 44 through 52
      removed outlier: 3.866A  pdb=" N   ASP C 284 " --> pdb=" O   LYS C 275 " (cutoff:3.500A)
    Processing sheet with id=AG2, first strand: chain 'C' and resid 81 through 82
    Processing sheet with id=AG3, first strand: chain 'C' and resid 129 through 132
      removed outlier: 5.948A  pdb=" N   GLU C 129 " --> pdb=" O   ALA C 160 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ALA C 160 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLN C 131 " --> pdb=" O   SER C 158 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'C' and resid 139 through 140
      removed outlier: 3.990A  pdb=" N   ASP C 139 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
    Processing sheet with id=AG5, first strand: chain 'C' and resid 308 through 316
      removed outlier: 4.397A  pdb=" N   VAL C 592 " --> pdb=" O   THR C 312 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASN C 314 " --> pdb=" O   GLY C 590 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLY C 590 " --> pdb=" O   ASN C 314 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   GLY C 591 " --> pdb=" O   GLN C 610 " (cutoff:3.500A)
    Processing sheet with id=AG6, first strand: chain 'C' and resid 321 through 325
      removed outlier: 4.204A  pdb=" N   GLU C 321 " --> pdb=" O   CYS C 535 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   ASP C 571 " --> pdb=" O   ILE C 584 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'C' and resid 351 through 355
    Processing sheet with id=AG8, first strand: chain 'C' and resid 358 through 359
      removed outlier: 6.567A  pdb=" N   CYS C 358 " --> pdb=" O   CYS C 522 " (cutoff:3.500A)
    Processing sheet with id=AG9, first strand: chain 'C' and resid 449 through 451
    Processing sheet with id=AH1, first strand: chain 'C' and resid 470 through 471
    Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 652
      removed outlier: 6.145A  pdb=" N   ALA C 669 " --> pdb=" O   PRO C 662 " (cutoff:3.500A)
    Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712
      removed outlier: 3.857A  pdb=" N   ALA C1075 " --> pdb=" O   PHE C1092 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   PHE C1092 " --> pdb=" O   ALA C1075 " (cutoff:3.500A)
    Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725
      removed outlier: 5.904A  pdb=" N   TYR C1064 " --> pdb=" O   HIS C1045 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   HIS C1045 " --> pdb=" O   TYR C1064 " (cutoff:3.500A)
    Processing sheet with id=AH5, first strand: chain 'C' and resid 730 through 733
      removed outlier: 4.464A  pdb=" N   LYS C 730 " --> pdb=" O   LEU C 858 " (cutoff:3.500A)
    Processing sheet with id=AH6, first strand: chain 'C' and resid 1117 through 1119

    1322 hydrogen bonds defined for protein.
    3486 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: 17.31

  Time building geometry restraints manager: 12.97 seconds

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

  Histogram of bond lengths:
        0.76 -     1.01: 2
        1.01 -     1.26: 4921
        1.26 -     1.50: 13997
        1.50 -     1.75: 12030
        1.75 -     2.00: 175
  Bond restraints: 31125
  Sorted by residual:
  bond pdb=" CG  PRO F   9 "
       pdb=" CD  PRO F   9 "
    ideal  model  delta    sigma   weight residual
    1.503  0.759  0.744 3.40e-02 8.65e+02 4.78e+02
  bond pdb=" CG  PRO D   9 "
       pdb=" CD  PRO D   9 "
    ideal  model  delta    sigma   weight residual
    1.503  0.894  0.609 3.40e-02 8.65e+02 3.21e+02
  bond pdb=" CB  PRO F   9 "
       pdb=" CG  PRO F   9 "
    ideal  model  delta    sigma   weight residual
    1.492  2.001 -0.509 5.00e-02 4.00e+02 1.04e+02
  bond pdb=" N   PRO H   9 "
       pdb=" CA  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.468  1.564 -0.096 1.20e-02 6.94e+03 6.44e+01
  bond pdb=" CB  PRO H   9 "
       pdb=" CG  PRO H   9 "
    ideal  model  delta    sigma   weight residual
    1.492  1.105  0.387 5.00e-02 4.00e+02 6.00e+01
  ... (remaining 31120 not shown)

  Histogram of bond angle deviations from ideal:
       51.20 -    76.96: 7
       76.96 -   102.71: 81
      102.71 -   128.46: 42121
      128.46 -   154.21: 147
      154.21 -   179.97: 1
  Bond angle restraints: 42357
  Sorted by residual:
  angle pdb=" N   PRO D   9 "
        pdb=" CD  PRO D   9 "
        pdb=" CG  PRO D   9 "
      ideal   model   delta    sigma   weight residual
     103.20   51.20   52.00 1.50e+00 4.44e-01 1.20e+03
  angle pdb=" N   PRO F   9 "
        pdb=" CD  PRO F   9 "
        pdb=" CG  PRO F   9 "
      ideal   model   delta    sigma   weight residual
     103.20   62.65   40.55 1.50e+00 4.44e-01 7.31e+02
  angle pdb=" N   PRO H   9 "
        pdb=" CD  PRO H   9 "
        pdb=" CG  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     103.20   67.36   35.84 1.50e+00 4.44e-01 5.71e+02
  angle pdb=" CB  PRO H   9 "
        pdb=" CG  PRO H   9 "
        pdb=" CD  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     106.10  179.97  -73.87 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" CA  PRO D   9 "
        pdb=" CB  PRO D   9 "
        pdb=" CG  PRO D   9 "
      ideal   model   delta    sigma   weight residual
     104.50   61.12   43.38 1.90e+00 2.77e-01 5.21e+02
  ... (remaining 42352 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 17724
       22.75 -    45.50: 896
       45.50 -    68.25: 160
       68.25 -    91.00: 70
       91.00 -   113.75: 2
  Dihedral angle restraints: 18852
    sinusoidal: 7632
      harmonic: 11220
  Sorted by residual:
  dihedral pdb=" N   PRO F   9 "
           pdb=" C   PRO F   9 "
           pdb=" CA  PRO F   9 "
           pdb=" CB  PRO F   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10   97.53   17.57     0      2.50e+00 1.60e-01 4.94e+01
  dihedral pdb=" CA  PRO D   9 "
           pdb=" CB  PRO D   9 "
           pdb=" CG  PRO D   9 "
           pdb=" CD  PRO D   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      38.00  151.75 -113.75     1      2.00e+01 2.50e-03 3.37e+01
  dihedral pdb=" N   PRO D   9 "
           pdb=" CG  PRO D   9 "
           pdb=" CD  PRO D   9 "
           pdb=" CB  PRO D   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  107.23  -77.23     1      1.50e+01 4.44e-03 3.32e+01
  ... (remaining 18849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 3625
       0.048 -    0.096: 974
       0.096 -    0.144: 276
       0.144 -    0.192: 10
       0.192 -    0.240: 2
  Chirality restraints: 4887
  Sorted by residual:
  chirality pdb=" CA  PRO H   9 "
            pdb=" N   PRO H   9 "
            pdb=" C   PRO H   9 "
            pdb=" CB  PRO H   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  PRO D   9 "
            pdb=" N   PRO D   9 "
            pdb=" C   PRO D   9 "
            pdb=" CB  PRO D   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.95   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  PRO F   9 "
            pdb=" N   PRO F   9 "
            pdb=" C   PRO F   9 "
            pdb=" CB  PRO F   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.89   -0.17 2.00e-01 2.50e+01 7.64e-01
  ... (remaining 4884 not shown)

  Planarity restraints: 5436
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H   8 "   -0.106 5.00e-02 4.00e+02   1.52e-01 3.68e+01
        pdb=" N   PRO H   9 "    0.262 5.00e-02 4.00e+02
        pdb=" CA  PRO H   9 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO H   9 "   -0.089 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D   8 "    0.086 5.00e-02 4.00e+02   1.23e-01 2.42e+01
        pdb=" N   PRO D   9 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO D   9 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO D   9 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  41 "    0.072 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO L  42 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO L  42 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO L  42 "    0.057 5.00e-02 4.00e+02
  ... (remaining 5433 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 255
        2.65 -     3.22: 26987
        3.22 -     3.78: 46994
        3.78 -     4.34: 69218
        4.34 -     4.90: 110180
  Nonbonded interactions: 253634
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 596 "
            pdb=" O   PRO C 597 "
     model   vdw
     2.093 2.440
  nonbonded pdb=" OG1 THR A 596 "
            pdb=" O   PRO A 597 "
     model   vdw
     2.093 2.440
  nonbonded pdb=" OG1 THR B 596 "
            pdb=" O   PRO B 597 "
     model   vdw
     2.094 2.440
  nonbonded pdb=" O   THR B 390 "
            pdb=" OG1 THR B 520 "
     model   vdw
     2.112 2.440
  nonbonded pdb=" O   THR C 390 "
            pdb=" OG1 THR C 520 "
     model   vdw
     2.112 2.440
  ... (remaining 253629 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:             0.020
  Extract box with map and model:          5.090
  Check model and map are aligned:         0.200
  Set scattering table:                    0.260
  Process input model:                     86.050
  Find NCS groups from input model:        1.920
  Set up NCS constraints:                  0.210
  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:12.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  107.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
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      :  0.008   0.744  31125  Z= 0.509
  Angle     :  0.869  73.867  42357  Z= 0.471
  Chirality :  0.046   0.240   4887
  Planarity :  0.005   0.152   5406
  Dihedral  : 14.579 113.749  11505
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.53 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.06 %
  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:  0.17 (0.13), residues: 3813
  helix:  1.93 (0.20), residues: 714
  sheet:  0.29 (0.15), residues: 1023
  loop : -0.61 (0.12), residues: 2076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.007   0.001   HIS A 516 
 PHE   0.015   0.001   PHE B 895 
 TYR   0.018   0.001   TYR C1064 
 ARG   0.002   0.000   ARG C1016 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 243
  time to evaluate  : 3.406 
Fit side-chains
REVERT: H   40 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7339 (ptt180)
REVERT: F    9 PRO cc_start: 0.6117 (OUTLIER) cc_final: 0.5888 (Cg_exo)
REVERT: F  101 ASP cc_start: 0.8005 (t0) cc_final: 0.7804 (t0)
REVERT: F  119 MET cc_start: 0.6791 (mtt) cc_final: 0.6381 (mpp)
REVERT: B  118 ASN cc_start: 0.7095 (t0) cc_final: 0.6701 (m110)
REVERT: B  150 MET cc_start: 0.6046 (tmm) cc_final: 0.5601 (pp-130)
REVERT: B  776 GLN cc_start: 0.8858 (tt0) cc_final: 0.8581 (tp40)
REVERT: B  897 MET cc_start: 0.9325 (mtp) cc_final: 0.9092 (mtp)
REVERT: B  932 GLN cc_start: 0.7847 (tt0) cc_final: 0.7640 (tt0)
REVERT: B 1070 LYS cc_start: 0.8608 (mttt) cc_final: 0.8290 (mtpp)
REVERT: C  150 MET cc_start: 0.6036 (tmm) cc_final: 0.5403 (pp-130)
REVERT: C  742 ASP cc_start: 0.8132 (p0) cc_final: 0.7931 (p0)
REVERT: C  776 GLN cc_start: 0.8888 (tt0) cc_final: 0.8672 (tp40)
REVERT: C 1070 LYS cc_start: 0.8632 (mttt) cc_final: 0.8244 (mtpp)
  outliers start: 36
  outliers final: 23
  residues processed: 273
  average time/residue: 1.3241
  time to fit residues: 434.3366
Evaluate side-chains
  249 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 224
  time to evaluate  : 3.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   40 ARG
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain F residue    9 PRO
Chi-restraints excluded: chain F residue   25 SER
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  782 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 321 optimal weight:    6.9990
   chunk 288 optimal weight:   20.0000
   chunk 160 optimal weight:   30.0000
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 298 optimal weight:   20.0000
   chunk 115 optimal weight:   30.0000
   chunk 181 optimal weight:   50.0000
   chunk 222 optimal weight:    9.9990
   chunk 345 optimal weight:   10.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 GLN
H 116 GLN
B 447 ASN
B 561 GLN
B 999 GLN
C 118 ASN
C 236 GLN
C 561 GLN
C 910 GLN
C 999 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.0533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093  31125  Z= 0.326
  Angle     :  0.603  14.627  42357  Z= 0.326
  Chirality :  0.048   0.202   4887
  Planarity :  0.005   0.054   5406
  Dihedral  :  5.792  51.036   4806
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.36 %
    Favored  : 87.53 %
  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:  0.12 (0.13), residues: 3813
  helix:  1.84 (0.20), residues: 714
  sheet:  0.27 (0.15), residues: 1008
  loop : -0.63 (0.12), residues: 2091

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  36 
 HIS   0.008   0.002   HIS C 516 
 PHE   0.022   0.002   PHE B 895 
 TYR   0.021   0.002   TYR C 753 
 ARG   0.005   0.001   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 231
  time to evaluate  : 3.480 
Fit side-chains
REVERT: A  455 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7886 (mtmt)
REVERT: A  643 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8026 (mtp180)
REVERT: D   40 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7476 (ptt180)
REVERT: E   40 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6633 (tt0)
REVERT: E   87 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6990 (m-30)
REVERT: F  119 MET cc_start: 0.6824 (mtt) cc_final: 0.6416 (mpp)
REVERT: B  118 ASN cc_start: 0.7172 (t0) cc_final: 0.6777 (m110)
REVERT: B  150 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5834 (mpt)
REVERT: B  643 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7842 (mtp180)
REVERT: B  776 GLN cc_start: 0.8793 (tt0) cc_final: 0.8520 (tp40)
REVERT: B  847 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7879 (mp)
REVERT: B  932 GLN cc_start: 0.7881 (tt0) cc_final: 0.7662 (tt0)
REVERT: B 1070 LYS cc_start: 0.8660 (mttt) cc_final: 0.8169 (mptt)
REVERT: C  150 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5385 (pp-130)
REVERT: C  169 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.7015 (m)
REVERT: C  643 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7866 (mtp180)
REVERT: C  742 ASP cc_start: 0.8165 (p0) cc_final: 0.7948 (p0)
REVERT: C 1070 LYS cc_start: 0.8644 (mttt) cc_final: 0.8274 (mtpp)
  outliers start: 71
  outliers final: 28
  residues processed: 285
  average time/residue: 1.3051
  time to fit residues: 449.8541
Evaluate side-chains
  264 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 4.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  116 GLN
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 192 optimal weight:    9.9990
   chunk 107 optimal weight:   30.0000
   chunk 287 optimal weight:   10.0000
   chunk 235 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 346 optimal weight:    3.9990
   chunk 374 optimal weight:    6.9990
   chunk 308 optimal weight:   10.0000
   chunk 343 optimal weight:   10.0000
   chunk 118 optimal weight:   30.0000
   chunk 278 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
A 625 GLN
A 999 GLN
H 116 GLN
B 447 ASN
B 561 GLN
C 118 ASN
C 561 GLN
C 625 GLN
C 999 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.0621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  31125  Z= 0.253
  Angle     :  0.544   6.341  42357  Z= 0.295
  Chirality :  0.046   0.168   4887
  Planarity :  0.004   0.042   5406
  Dihedral  :  5.435  54.773   4783
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.56 %
    Favored  : 87.47 %
  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:  0.20 (0.13), residues: 3813
  helix:  2.06 (0.20), residues: 693
  sheet:  0.31 (0.15), residues: 1008
  loop : -0.60 (0.12), residues: 2112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.007   0.001   HIS C 516 
 PHE   0.019   0.002   PHE B 895 
 TYR   0.019   0.002   TYR A1064 
 ARG   0.005   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 237
  time to evaluate  : 3.357 
Fit side-chains
REVERT: A  455 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7881 (mtmt)
REVERT: A  643 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7709 (mtp180)
REVERT: D   40 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7438 (ptt180)
REVERT: E   40 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6601 (tt0)
REVERT: E   87 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7030 (m-30)
REVERT: F  119 MET cc_start: 0.6801 (mtt) cc_final: 0.6428 (mpp)
REVERT: B  118 ASN cc_start: 0.7120 (t0) cc_final: 0.6743 (m110)
REVERT: B  150 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5777 (mpt)
REVERT: B  455 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7837 (mtmt)
REVERT: B  643 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7227 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8793 (tt0) cc_final: 0.8487 (tp40)
REVERT: B  847 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7885 (mp)
REVERT: B  932 GLN cc_start: 0.7946 (tt0) cc_final: 0.7697 (tt0)
REVERT: B 1070 LYS cc_start: 0.8658 (mttt) cc_final: 0.8173 (mptt)
REVERT: C  150 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5274 (pp-130)
REVERT: C  169 SER cc_start: 0.7310 (OUTLIER) cc_final: 0.7076 (m)
REVERT: C  643 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7637 (mtp180)
REVERT: C  742 ASP cc_start: 0.8143 (p0) cc_final: 0.7935 (p0)
REVERT: C 1070 LYS cc_start: 0.8623 (mttt) cc_final: 0.8259 (mtpp)
  outliers start: 66
  outliers final: 30
  residues processed: 286
  average time/residue: 1.2733
  time to fit residues: 440.2095
Evaluate side-chains
  269 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 229
  time to evaluate  : 3.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 342 optimal weight:   10.0000
   chunk 260 optimal weight:    5.9990
   chunk 179 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 165 optimal weight:   20.0000
   chunk 232 optimal weight:    6.9990
   chunk 347 optimal weight:    0.7980
   chunk 368 optimal weight:    6.9990
   chunk 181 optimal weight:   40.0000
   chunk 329 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
A 999 GLN
H 116 GLN
L  40 GLN
B 447 ASN
B 561 GLN
B 625 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  31125  Z= 0.251
  Angle     :  0.546   7.276  42357  Z= 0.295
  Chirality :  0.046   0.169   4887
  Planarity :  0.004   0.042   5406
  Dihedral  :  5.407  57.411   4779
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.65 %
    Favored  : 87.17 %
  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:  0.21 (0.13), residues: 3813
  helix:  2.01 (0.20), residues: 696
  sheet:  0.32 (0.15), residues: 1008
  loop : -0.58 (0.12), residues: 2109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.007   0.001   HIS C 516 
 PHE   0.019   0.002   PHE B 895 
 TYR   0.019   0.002   TYR A1064 
 ARG   0.006   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 233
  time to evaluate  : 3.462 
Fit side-chains
REVERT: A  643 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8044 (mtp180)
REVERT: A  961 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8192 (mtpt)
REVERT: D   40 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7480 (ptt180)
REVERT: E   40 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6434 (tt0)
REVERT: E   87 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7068 (m-30)
REVERT: F  119 MET cc_start: 0.6796 (mtt) cc_final: 0.6425 (mpp)
REVERT: G   49 MET cc_start: 0.7765 (mmp) cc_final: 0.7455 (mmp)
REVERT: B  118 ASN cc_start: 0.7163 (t0) cc_final: 0.6785 (m110)
REVERT: B  150 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5707 (mpt)
REVERT: B  437 LYS cc_start: 0.8150 (mttt) cc_final: 0.7941 (mtpt)
REVERT: B  455 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7838 (mtmt)
REVERT: B  643 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7205 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8830 (tt0) cc_final: 0.8498 (tp40)
REVERT: B  847 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7886 (mp)
REVERT: B  932 GLN cc_start: 0.7945 (tt0) cc_final: 0.7694 (tt0)
REVERT: B  961 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7991 (mppt)
REVERT: B 1070 LYS cc_start: 0.8652 (mttt) cc_final: 0.8173 (mptt)
REVERT: C  118 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6826 (m110)
REVERT: C  138 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6723 (mp)
REVERT: C  169 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7136 (m)
REVERT: C  318 GLN cc_start: 0.8303 (mm110) cc_final: 0.8056 (mm110)
REVERT: C  643 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7630 (mtp180)
REVERT: C  742 ASP cc_start: 0.8133 (p0) cc_final: 0.7911 (p0)
REVERT: C 1070 LYS cc_start: 0.8625 (mttt) cc_final: 0.8262 (mtpp)
  outliers start: 73
  outliers final: 35
  residues processed: 290
  average time/residue: 1.3510
  time to fit residues: 470.5026
Evaluate side-chains
  279 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 231
  time to evaluate  : 3.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 306 optimal weight:   10.0000
   chunk 209 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 274 optimal weight:    0.0040
   chunk 151 optimal weight:   30.0000
   chunk 314 optimal weight:    0.0270
   chunk 254 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 188 optimal weight:   30.0000
   chunk 330 optimal weight:   30.0000
   chunk 92 optimal weight:    7.9990
   overall best weight:    5.2056

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A 268 GLN
A 999 GLN
H 116 GLN
B 561 GLN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.0773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  31125  Z= 0.238
  Angle     :  0.535   7.752  42357  Z= 0.289
  Chirality :  0.046   0.161   4887
  Planarity :  0.004   0.040   5406
  Dihedral  :  5.369  58.142   4779
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.22 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.23 (0.13), residues: 3813
  helix:  2.22 (0.20), residues: 675
  sheet:  0.32 (0.15), residues: 1008
  loop : -0.60 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.007   0.001   HIS C 516 
 PHE   0.019   0.002   PHE B 895 
 TYR   0.019   0.001   TYR A1064 
 ARG   0.006   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 237
  time to evaluate  : 3.717 
Fit side-chains
REVERT: A  169 SER cc_start: 0.7250 (OUTLIER) cc_final: 0.7007 (m)
REVERT: A  643 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7682 (mtp180)
REVERT: A  792 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.6193 (tmtt)
REVERT: A  961 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (mtpt)
REVERT: L   40 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.5652 (tp40)
REVERT: D   40 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7503 (ptt180)
REVERT: E   40 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6398 (tt0)
REVERT: E   87 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7067 (m-30)
REVERT: F  119 MET cc_start: 0.6789 (mtt) cc_final: 0.6424 (mpp)
REVERT: G   49 MET cc_start: 0.7759 (mmp) cc_final: 0.7475 (mmp)
REVERT: B  118 ASN cc_start: 0.7165 (t0) cc_final: 0.6806 (m110)
REVERT: B  150 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5705 (mpt)
REVERT: B  437 LYS cc_start: 0.8127 (mttt) cc_final: 0.7909 (mtpt)
REVERT: B  455 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7834 (mtmt)
REVERT: B  643 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7146 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8826 (tt0) cc_final: 0.8498 (tp40)
REVERT: B  847 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: B  932 GLN cc_start: 0.7931 (tt0) cc_final: 0.7674 (tt0)
REVERT: B  961 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7982 (mppt)
REVERT: B 1070 LYS cc_start: 0.8652 (mttt) cc_final: 0.8178 (mptt)
REVERT: C  118 ASN cc_start: 0.7189 (t0) cc_final: 0.6808 (m110)
REVERT: C  138 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6667 (mp)
REVERT: C  169 SER cc_start: 0.7364 (OUTLIER) cc_final: 0.7128 (m)
REVERT: C  437 LYS cc_start: 0.8111 (mttt) cc_final: 0.7906 (mtpt)
REVERT: C  643 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7632 (mtp180)
REVERT: C  742 ASP cc_start: 0.8136 (p0) cc_final: 0.7915 (p0)
REVERT: C 1070 LYS cc_start: 0.8631 (mttt) cc_final: 0.8266 (mtpp)
  outliers start: 72
  outliers final: 40
  residues processed: 296
  average time/residue: 1.3397
  time to fit residues: 474.9460
Evaluate side-chains
  284 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 229
  time to evaluate  : 3.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LYS
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  938 THR
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 123 optimal weight:   20.0000
   chunk 331 optimal weight:    9.9990
   chunk 72 optimal weight:    0.3980
   chunk 216 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 368 optimal weight:    5.9990
   chunk 306 optimal weight:   20.0000
   chunk 170 optimal weight:   30.0000
   chunk 30 optimal weight:    0.0770
   chunk 121 optimal weight:   50.0000
   chunk 193 optimal weight:    7.9990
   overall best weight:    4.8944

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
A 999 GLN
H 116 GLN
B 561 GLN
C  23 GLN
C 118 ASN
C 122 ASN
C 561 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  31125  Z= 0.226
  Angle     :  0.530   9.160  42357  Z= 0.285
  Chirality :  0.045   0.160   4887
  Planarity :  0.004   0.038   5406
  Dihedral  :  5.307  58.950   4779
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.43 %
    Favored  : 86.33 %
  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:  0.28 (0.13), residues: 3813
  helix:  2.26 (0.20), residues: 675
  sheet:  0.34 (0.15), residues: 1008
  loop : -0.57 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.006   0.001   HIS C 516 
 PHE   0.018   0.001   PHE B 895 
 TYR   0.019   0.001   TYR A1064 
 ARG   0.004   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 235
  time to evaluate  : 3.296 
Fit side-chains
REVERT: A  169 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6943 (m)
REVERT: A  437 LYS cc_start: 0.8186 (mttt) cc_final: 0.7959 (mtpt)
REVERT: A  643 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7667 (mtp180)
REVERT: A  792 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.6200 (tmtt)
REVERT: A  961 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8178 (mtpt)
REVERT: L   40 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.5704 (tp40)
REVERT: D   40 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7490 (ptt180)
REVERT: E   40 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6310 (tt0)
REVERT: E   87 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7067 (m-30)
REVERT: G   49 MET cc_start: 0.7738 (mmp) cc_final: 0.7401 (mmp)
REVERT: B  118 ASN cc_start: 0.7165 (t0) cc_final: 0.6812 (m110)
REVERT: B  150 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5718 (mpt)
REVERT: B  332 LEU cc_start: 0.7948 (mm) cc_final: 0.7631 (mm)
REVERT: B  437 LYS cc_start: 0.8114 (mttt) cc_final: 0.7893 (mtpt)
REVERT: B  455 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7825 (mtmt)
REVERT: B  643 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7152 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8829 (tt0) cc_final: 0.8502 (tp40)
REVERT: B  847 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: B  932 GLN cc_start: 0.7974 (tt0) cc_final: 0.7720 (tt0)
REVERT: B  961 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7978 (mppt)
REVERT: B 1070 LYS cc_start: 0.8657 (mttt) cc_final: 0.8185 (mptt)
REVERT: C  138 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6699 (mp)
REVERT: C  169 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.7122 (m)
REVERT: C  437 LYS cc_start: 0.8122 (mttt) cc_final: 0.7904 (mtpt)
REVERT: C  643 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7623 (mtp180)
REVERT: C  742 ASP cc_start: 0.8130 (p0) cc_final: 0.7910 (p0)
REVERT: C 1070 LYS cc_start: 0.8628 (mttt) cc_final: 0.8264 (mtpp)
  outliers start: 75
  outliers final: 42
  residues processed: 296
  average time/residue: 1.3636
  time to fit residues: 484.9014
Evaluate side-chains
  289 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 232
  time to evaluate  : 3.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LYS
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  938 THR
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 355 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 210 optimal weight:    5.9990
   chunk 269 optimal weight:    8.9990
   chunk 208 optimal weight:   20.0000
   chunk 310 optimal weight:    8.9990
   chunk 205 optimal weight:    7.9990
   chunk 367 optimal weight:   10.0000
   chunk 229 optimal weight:    1.9990
   chunk 223 optimal weight:    0.0060
   chunk 169 optimal weight:    8.9990
   overall best weight:    4.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
A 999 GLN
H 116 GLN
D 116 GLN
B  23 GLN
B 561 GLN
B 910 GLN
B 999 GLN
C  23 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  31125  Z= 0.208
  Angle     :  0.517   9.557  42357  Z= 0.278
  Chirality :  0.045   0.158   4887
  Planarity :  0.004   0.035   5406
  Dihedral  :  5.224  58.948   4779
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.70 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.13), residues: 3813
  helix:  2.31 (0.20), residues: 675
  sheet:  0.35 (0.15), residues: 1008
  loop : -0.54 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.006   0.001   HIS C 516 
 PHE   0.017   0.001   PHE B 895 
 TYR   0.018   0.001   TYR A1064 
 ARG   0.007   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 243
  time to evaluate  : 3.255 
Fit side-chains
REVERT: A  169 SER cc_start: 0.7155 (OUTLIER) cc_final: 0.6915 (m)
REVERT: A  437 LYS cc_start: 0.8180 (mttt) cc_final: 0.7943 (mtpt)
REVERT: A  643 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7681 (mtp180)
REVERT: A  792 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.6192 (tmtt)
REVERT: A  961 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7971 (mppt)
REVERT: L   40 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.5680 (tp40)
REVERT: D   40 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7496 (ptt180)
REVERT: E   40 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6287 (tt0)
REVERT: E   87 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7076 (m-30)
REVERT: G   49 MET cc_start: 0.7708 (mmp) cc_final: 0.7320 (mmp)
REVERT: B  118 ASN cc_start: 0.7137 (t0) cc_final: 0.6782 (m110)
REVERT: B  150 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5824 (mpt)
REVERT: B  355 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7958 (mp)
REVERT: B  437 LYS cc_start: 0.8091 (mttt) cc_final: 0.7862 (mtpt)
REVERT: B  455 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7824 (mtmt)
REVERT: B  643 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7160 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8515 (tp40)
REVERT: B  847 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7877 (mp)
REVERT: B  932 GLN cc_start: 0.7976 (tt0) cc_final: 0.7717 (tt0)
REVERT: B  961 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7966 (mppt)
REVERT: B 1070 LYS cc_start: 0.8654 (mttt) cc_final: 0.8184 (mptt)
REVERT: C  138 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6744 (mp)
REVERT: C  169 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.7132 (m)
REVERT: C  318 GLN cc_start: 0.8225 (mm110) cc_final: 0.7983 (mm110)
REVERT: C  643 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7609 (mtp180)
REVERT: C  742 ASP cc_start: 0.8129 (p0) cc_final: 0.7911 (p0)
REVERT: C 1070 LYS cc_start: 0.8644 (mttt) cc_final: 0.8273 (mtpp)
  outliers start: 69
  outliers final: 41
  residues processed: 299
  average time/residue: 1.3310
  time to fit residues: 478.3323
Evaluate side-chains
  289 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 231
  time to evaluate  : 3.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLN
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LYS
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  938 THR
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 227 optimal weight:    7.9990
   chunk 146 optimal weight:   50.0000
   chunk 219 optimal weight:    8.9990
   chunk 110 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0060
   chunk 71 optimal weight:    3.9990
   chunk 233 optimal weight:    0.0980
   chunk 250 optimal weight:    9.9990
   chunk 181 optimal weight:   50.0000
   chunk 34 optimal weight:    8.9990
   chunk 288 optimal weight:    5.9990
   overall best weight:    3.6202

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
A 999 GLN
H 116 GLN
F 116 GLN
B  23 GLN
B 561 GLN
B 999 GLN
C  23 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.0917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  31125  Z= 0.181
  Angle     :  0.502  10.199  42357  Z= 0.268
  Chirality :  0.044   0.156   4887
  Planarity :  0.004   0.035   5406
  Dihedral  :  5.107  58.625   4779
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.82 %
    Favored  : 86.06 %
  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:  0.38 (0.13), residues: 3813
  helix:  2.37 (0.20), residues: 675
  sheet:  0.38 (0.15), residues: 1008
  loop : -0.49 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.006   0.001   HIS C 516 
 PHE   0.015   0.001   PHE B 895 
 TYR   0.018   0.001   TYR A1064 
 ARG   0.009   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 237
  time to evaluate  : 3.900 
Fit side-chains
REVERT: A  169 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6934 (m)
REVERT: A  355 ILE cc_start: 0.8219 (mm) cc_final: 0.8014 (mt)
REVERT: A  437 LYS cc_start: 0.8168 (mttt) cc_final: 0.7932 (mtpt)
REVERT: A  643 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7674 (mtp180)
REVERT: A  961 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7959 (mppt)
REVERT: L   40 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.5596 (tp40)
REVERT: D   40 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7493 (ptt180)
REVERT: E   40 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6250 (tt0)
REVERT: E   87 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7079 (m-30)
REVERT: G   49 MET cc_start: 0.7678 (mmp) cc_final: 0.7370 (mmp)
REVERT: B  118 ASN cc_start: 0.7144 (t0) cc_final: 0.6775 (m110)
REVERT: B  150 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.5793 (mpt)
REVERT: B  318 GLN cc_start: 0.8181 (mm110) cc_final: 0.7950 (mm110)
REVERT: B  332 LEU cc_start: 0.7931 (mm) cc_final: 0.7632 (mm)
REVERT: B  437 LYS cc_start: 0.8071 (mttt) cc_final: 0.7843 (mtpt)
REVERT: B  455 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7827 (mtmt)
REVERT: B  643 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7194 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8498 (tp40)
REVERT: B  847 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7877 (mp)
REVERT: B  932 GLN cc_start: 0.7963 (tt0) cc_final: 0.7709 (tt0)
REVERT: B  961 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7960 (mppt)
REVERT: B 1070 LYS cc_start: 0.8636 (mttt) cc_final: 0.8168 (mptt)
REVERT: C  118 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6816 (m110)
REVERT: C  138 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6763 (mp)
REVERT: C  150 MET cc_start: 0.5936 (tmm) cc_final: 0.4953 (pp-130)
REVERT: C  169 SER cc_start: 0.7357 (OUTLIER) cc_final: 0.7145 (m)
REVERT: C  332 LEU cc_start: 0.7837 (mm) cc_final: 0.7593 (mm)
REVERT: C  643 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7597 (mtp180)
REVERT: C  742 ASP cc_start: 0.8129 (p0) cc_final: 0.7912 (p0)
REVERT: C 1070 LYS cc_start: 0.8637 (mttt) cc_final: 0.8266 (mtpp)
  outliers start: 71
  outliers final: 38
  residues processed: 295
  average time/residue: 1.3285
  time to fit residues: 469.9211
Evaluate side-chains
  288 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 234
  time to evaluate  : 3.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  938 THR
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 334 optimal weight:    9.9990
   chunk 351 optimal weight:   20.0000
   chunk 320 optimal weight:    6.9990
   chunk 342 optimal weight:    0.6980
   chunk 205 optimal weight:    0.6980
   chunk 149 optimal weight:   30.0000
   chunk 268 optimal weight:    4.9990
   chunk 105 optimal weight:   40.0000
   chunk 309 optimal weight:    9.9990
   chunk 323 optimal weight:    2.9990
   chunk 341 optimal weight:    1.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
A 268 GLN
A 999 GLN
H 116 GLN
L  40 GLN
F 116 GLN
B 561 GLN
B 999 GLN
C  23 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  31125  Z= 0.141
  Angle     :  0.479  10.539  42357  Z= 0.255
  Chirality :  0.043   0.153   4887
  Planarity :  0.003   0.034   5406
  Dihedral  :  4.945  58.111   4779
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.32 %
    Favored  : 86.00 %
  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:  0.50 (0.13), residues: 3813
  helix:  2.48 (0.20), residues: 675
  sheet:  0.48 (0.16), residues: 978
  loop : -0.42 (0.12), residues: 2160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F  36 
 HIS   0.005   0.001   HIS C 516 
 PHE   0.015   0.001   PHE C 562 
 TYR   0.016   0.001   TYR A1064 
 ARG   0.007   0.000   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 239
  time to evaluate  : 3.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.7168 (OUTLIER) cc_final: 0.6915 (m)
REVERT: A  437 LYS cc_start: 0.8171 (mttt) cc_final: 0.7935 (mtpt)
REVERT: A  643 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7655 (mtp180)
REVERT: D   40 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7495 (ptt180)
REVERT: D  116 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6331 (pt0)
REVERT: E   40 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6218 (tt0)
REVERT: E   87 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7064 (m-30)
REVERT: G   49 MET cc_start: 0.7661 (mmp) cc_final: 0.7258 (mmp)
REVERT: B  118 ASN cc_start: 0.7129 (t0) cc_final: 0.6731 (m110)
REVERT: B  150 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5814 (mpt)
REVERT: B  332 LEU cc_start: 0.7917 (mm) cc_final: 0.7622 (mm)
REVERT: B  437 LYS cc_start: 0.8101 (mttt) cc_final: 0.7857 (mtpt)
REVERT: B  455 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7834 (mtmt)
REVERT: B  643 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7125 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8479 (tp40)
REVERT: B  847 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7874 (mp)
REVERT: B  932 GLN cc_start: 0.7968 (tt0) cc_final: 0.7723 (tt0)
REVERT: B  961 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7950 (mppt)
REVERT: B 1070 LYS cc_start: 0.8618 (mttt) cc_final: 0.8296 (mtpp)
REVERT: C  138 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6776 (mp)
REVERT: C  169 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.7086 (m)
REVERT: C  318 GLN cc_start: 0.8233 (mm110) cc_final: 0.8027 (mm110)
REVERT: C  332 LEU cc_start: 0.7830 (mm) cc_final: 0.7583 (mm)
REVERT: C  643 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7596 (mtp180)
REVERT: C  742 ASP cc_start: 0.8116 (p0) cc_final: 0.7900 (p0)
REVERT: C 1070 LYS cc_start: 0.8621 (mttt) cc_final: 0.8253 (mtpp)
  outliers start: 56
  outliers final: 28
  residues processed: 281
  average time/residue: 1.3749
  time to fit residues: 463.1745
Evaluate side-chains
  274 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 232
  time to evaluate  : 3.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  983 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  116 GLN
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 224 optimal weight:    5.9990
   chunk 361 optimal weight:   20.0000
   chunk 220 optimal weight:   20.0000
   chunk 171 optimal weight:   20.0000
   chunk 251 optimal weight:    8.9990
   chunk 379 optimal weight:    5.9990
   chunk 349 optimal weight:    4.9990
   chunk 302 optimal weight:   30.0000
   chunk 31 optimal weight:    6.9990
   chunk 233 optimal weight:   10.0000
   chunk 185 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
A 268 GLN
** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 GLN
H 116 GLN
F 116 GLN
B 122 ASN
B 561 GLN
B 999 GLN
C  23 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.0957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  31125  Z= 0.262
  Angle     :  0.549  10.780  42357  Z= 0.295
  Chirality :  0.046   0.170   4887
  Planarity :  0.004   0.042   5406
  Dihedral  :  5.321  59.054   4779
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.41 %
    Favored  : 85.97 %
  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:  0.34 (0.13), residues: 3813
  helix:  2.25 (0.20), residues: 675
  sheet:  0.39 (0.15), residues: 1008
  loop : -0.51 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  36 
 HIS   0.007   0.001   HIS C 516 
 PHE   0.019   0.002   PHE B 895 
 TYR   0.020   0.002   TYR A1064 
 ARG   0.007   0.001   ARG B 316 

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

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

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7626 Ramachandran restraints generated.
    3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 235
  time to evaluate  : 3.460 
Fit side-chains
REVERT: A  169 SER cc_start: 0.7176 (OUTLIER) cc_final: 0.6929 (m)
REVERT: A  437 LYS cc_start: 0.8195 (mttt) cc_final: 0.7950 (mtpt)
REVERT: A  643 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8037 (mtp180)
REVERT: A  792 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.6375 (tttm)
REVERT: A  961 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (mtpt)
REVERT: D   40 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7498 (ptt180)
REVERT: E   40 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6384 (tt0)
REVERT: E   87 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7093 (m-30)
REVERT: F  101 ASP cc_start: 0.7997 (t0) cc_final: 0.7785 (t0)
REVERT: G   49 MET cc_start: 0.7697 (mmp) cc_final: 0.7378 (mmp)
REVERT: B  118 ASN cc_start: 0.7168 (t0) cc_final: 0.6822 (m110)
REVERT: B  150 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5778 (mpt)
REVERT: B  332 LEU cc_start: 0.7946 (mm) cc_final: 0.7659 (mm)
REVERT: B  437 LYS cc_start: 0.8096 (mttt) cc_final: 0.7858 (mtpt)
REVERT: B  643 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7183 (mpp-170)
REVERT: B  776 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8499 (tp40)
REVERT: B  847 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: B  932 GLN cc_start: 0.7970 (tt0) cc_final: 0.7708 (tt0)
REVERT: B  961 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7988 (mppt)
REVERT: B 1070 LYS cc_start: 0.8654 (mttt) cc_final: 0.8176 (mptt)
REVERT: C  138 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6792 (mp)
REVERT: C  150 MET cc_start: 0.5941 (tmm) cc_final: 0.4953 (pp-130)
REVERT: C  169 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.7174 (m)
REVERT: C  332 LEU cc_start: 0.7798 (mm) cc_final: 0.7567 (mm)
REVERT: C  643 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7623 (mtp180)
REVERT: C  742 ASP cc_start: 0.8126 (p0) cc_final: 0.7910 (p0)
REVERT: C 1070 LYS cc_start: 0.8651 (mttt) cc_final: 0.8282 (mtpp)
  outliers start: 54
  outliers final: 31
  residues processed: 277
  average time/residue: 1.3971
  time to fit residues: 465.1643
Evaluate side-chains
  275 residues out of total 3351 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 229
  time to evaluate  : 3.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 ARG
Chi-restraints excluded: chain A residue  792 LYS
Chi-restraints excluded: chain A residue  961 LYS
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  116 GLN
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   40 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue   87 ASP
Chi-restraints excluded: chain F residue   37 SER
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   10 VAL
Chi-restraints excluded: chain G residue   36 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   84 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  776 GLN
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  960 VAL
Chi-restraints excluded: chain B residue  961 LYS
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  169 SER
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  596 THR
Chi-restraints excluded: chain C residue  643 ARG
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  960 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 381
   random chunks:
   chunk 240 optimal weight:    0.9990
   chunk 321 optimal weight:    0.2980
   chunk 92 optimal weight:    8.9990
   chunk 278 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 302 optimal weight:   20.0000
   chunk 126 optimal weight:   20.0000
   chunk 310 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
A 268 GLN
A 999 GLN
H 116 GLN
B 561 GLN
B 999 GLN
C  23 GLN
C 118 ASN
C 561 GLN
C 999 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.187837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114386 restraints weight = 27917.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.13
r_work: 0.3087 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  31125  Z= 0.187
  Angle     :  0.506  10.690  42357  Z= 0.271
  Chirality :  0.044   0.155   4887
  Planarity :  0.004   0.037   5406
  Dihedral  :  5.140  58.980   4779
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.29 %
    Favored  : 86.03 %
  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:  0.40 (0.13), residues: 3813
  helix:  2.34 (0.20), residues: 675
  sheet:  0.42 (0.15), residues: 1008
  loop : -0.48 (0.12), residues: 2130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  36 
 HIS   0.006   0.001   HIS C 516 
 PHE   0.016   0.001   PHE C 562 
 TYR   0.018   0.001   TYR A1064 
 ARG   0.007   0.000   ARG B 316 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10096.36 seconds
wall clock time: 182 minutes 51.33 seconds (10971.33 seconds total)