Starting phenix.real_space_refine
on Fri Aug  9 22:12:16 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6h_23696/08_2024/7m6h_23696_neut.cif"
  }
  resolution = 4.0
  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=  -0.001 sd=   0.017
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     127      5.16       5
     C   17404      2.51       5
     N    4534      2.21       5
     O    5314      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  306": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  324": "OE1" <-> "OE2"
    Residue "A PHE  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  660": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  800": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  917": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1144": "OE1" <-> "OE2"
    Residue "B PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  505": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  737": "OD1" <-> "OD2"
    Residue "B PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  797": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  904": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU 1017": "OE1" <-> "OE2"
    Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  111": "OD1" <-> "OD2"
    Residue "C PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  309": "OE1" <-> "OE2"
    Residue "C PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  420": "OD1" <-> "OD2"
    Residue "C GLU  465": "OE1" <-> "OE2"
    Residue "C PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  695": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  718": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  819": "OE1" <-> "OE2"
    Residue "C PHE  898": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  917": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU 1111": "OE1" <-> "OE2"
    Residue "C GLU 1144": "OE1" <-> "OE2"
    Residue "D TYR   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   85": "OE1" <-> "OE2"
    Residue "D TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE   46": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   87": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 27379
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 7823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1002, 7823
          Classifications: {'peptide': 1002}
          Link IDs: {'PTRANS': 49, 'TRANS': 952}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 7823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1002, 7823
          Classifications: {'peptide': 1002}
          Link IDs: {'PTRANS': 49, 'TRANS': 952}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 7823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1002, 7823
          Classifications: {'peptide': 1002}
          Link IDs: {'PTRANS': 49, 'TRANS': 952}
          Chain breaks: 7
    Chain: "D"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 953
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "E"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 953
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "F"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 806
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
    Chain: "G"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 806
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
    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: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
    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: 14.79, per 1000 atoms: 0.54
  Number of scatterers: 27379
  At special positions: 0
  Unit cell: (134.695, 143.385, 191.18, 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     127     16.00
     O    5314      8.00
     N    4534      7.00
     C   17404      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=43, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=1.45
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=1.99
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 122 "
      " NAG A1303 " - " ASN A 331 "
      " NAG A1304 " - " ASN A 343 "
      " NAG A1305 " - " ASN A 616 "
      " NAG A1306 " - " ASN A 709 "
      " NAG A1307 " - " ASN A 717 "
      " NAG A1308 " - " ASN A 801 "
      " NAG A1309 " - " ASN A1074 "
      " NAG B1301 " - " ASN B 234 "
      " NAG B1302 " - " ASN B 282 "
      " NAG B1303 " - " ASN B 616 "
      " NAG B1304 " - " ASN B 709 "
      " NAG B1305 " - " ASN B 717 "
      " NAG B1306 " - " ASN B 801 "
      " NAG B1307 " - " ASN B1134 "
      " NAG B1308 " - " ASN B 331 "
      " NAG C1301 " - " ASN A 282 "
      " NAG C1302 " - " ASN C 122 "
      " NAG C1303 " - " ASN C 234 "
      " NAG C1304 " - " ASN C 282 "
      " NAG C1305 " - " ASN C 165 "
      " NAG C1306 " - " ASN C 616 "
      " NAG C1307 " - " ASN C 709 "
      " NAG C1308 " - " ASN C 717 "
      " NAG C1309 " - " ASN C 801 "
      " NAG C1310 " - " ASN C 331 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 11.08
  Conformation dependent library (CDL) restraints added in 5.0 seconds
  

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6458

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      21.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.529A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   THR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 3.581A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 737 through 743
    Processing helix  chain 'A' and resid 747 through 754
    Processing helix  chain 'A' and resid 755 through 757
      No H-bonds generated for 'chain 'A' and resid 755 through 757'
    Processing helix  chain 'A' and resid 758 through 782
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 3.560A  pdb=" N   LYS A 825 " --> pdb=" O   LEU A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 885
    Processing helix  chain 'A' and resid 886 through 891
      removed outlier: 3.902A  pdb=" N   ALA A 890 " --> pdb=" O   TRP A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 908
    Processing helix  chain 'A' and resid 913 through 919
    Processing helix  chain 'A' and resid 919 through 941
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing helix  chain 'A' and resid 945 through 965
      removed outlier: 4.378A  pdb=" N   VAL A 951 " --> pdb=" O   LYS A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 985 through 1031
      removed outlier: 3.638A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1147
    Processing helix  chain 'B' and resid 294 through 303
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.528A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.191A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 739 through 744
    Processing helix  chain 'B' and resid 746 through 755
    Processing helix  chain 'B' and resid 758 through 782
    Processing helix  chain 'B' and resid 816 through 825
    Processing helix  chain 'B' and resid 866 through 884
    Processing helix  chain 'B' and resid 886 through 891
      removed outlier: 3.681A  pdb=" N   ALA B 890 " --> pdb=" O   TRP B 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 909
      removed outlier: 3.688A  pdb=" N   ILE B 909 " --> pdb=" O   ARG B 905 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 913 through 919
      removed outlier: 3.707A  pdb=" N   TYR B 917 " --> pdb=" O   GLN B 913 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 919 through 941
    Processing helix  chain 'B' and resid 942 through 944
      No H-bonds generated for 'chain 'B' and resid 942 through 944'
    Processing helix  chain 'B' and resid 945 through 966
      removed outlier: 4.124A  pdb=" N   VAL B 951 " --> pdb=" O   LYS B 947 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 976 through 984
    Processing helix  chain 'B' and resid 985 through 1033
      removed outlier: 4.297A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1140 through 1147
      removed outlier: 4.102A  pdb=" N   GLU B1144 " --> pdb=" O   PRO B1140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 304
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 366 through 371
    Processing helix  chain 'C' and resid 502 through 506
      removed outlier: 3.875A  pdb=" N   GLN C 506 " --> pdb=" O   VAL C 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 737 through 744
    Processing helix  chain 'C' and resid 747 through 755
    Processing helix  chain 'C' and resid 758 through 782
    Processing helix  chain 'C' and resid 816 through 825
    Processing helix  chain 'C' and resid 866 through 884
    Processing helix  chain 'C' and resid 886 through 891
      removed outlier: 3.792A  pdb=" N   ALA C 890 " --> pdb=" O   TRP C 886 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 897 through 908
    Processing helix  chain 'C' and resid 912 through 918
      removed outlier: 4.142A  pdb=" N   LEU C 916 " --> pdb=" O   THR C 912 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 919 through 941
    Processing helix  chain 'C' and resid 945 through 966
      removed outlier: 4.127A  pdb=" N   VAL C 951 " --> pdb=" O   LYS C 947 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 976 through 984
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 4.245A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1141 through 1147
    Processing helix  chain 'D' and resid 83 through 87
      removed outlier: 3.640A  pdb=" N   ASP D  86 " --> pdb=" O   ARG D  83 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   THR D  87 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 83 through 87'
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.796A  pdb=" N   SER E  31 " --> pdb=" O   THR E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 87
      removed outlier: 3.815A  pdb=" N   ASP E  86 " --> pdb=" O   ARG E  83 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR E  87 " --> pdb=" O   SER E  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 83 through 87'
    Processing helix  chain 'F' and resid 26 through 30
      removed outlier: 4.088A  pdb=" N   ALA F  29 " --> pdb=" O   SER F  27A" (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1452 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: 6.62

  Time building geometry restraints manager: 12.13 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 4474
        1.31 -     1.44: 7794
        1.44 -     1.57: 15557
        1.57 -     1.70: 1
        1.70 -     1.83: 161
  Bond restraints: 27987
  Sorted by residual:
  bond pdb=" C   VAL A 320 "
       pdb=" N   GLN A 321 "
    ideal  model  delta    sigma   weight residual
    1.326  1.237  0.090 1.84e-02 2.95e+03 2.37e+01
  bond pdb=" C   ARG C 357 "
       pdb=" O   ARG C 357 "
    ideal  model  delta    sigma   weight residual
    1.234  1.175  0.059 1.26e-02 6.30e+03 2.19e+01
  bond pdb=" N   PRO D 112 "
       pdb=" CD  PRO D 112 "
    ideal  model  delta    sigma   weight residual
    1.473  1.522 -0.049 1.40e-02 5.10e+03 1.24e+01
  bond pdb=" N   PRO E 112 "
       pdb=" CD  PRO E 112 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.19e+01
  bond pdb=" N   ILE C 402 "
       pdb=" CA  ILE C 402 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.11e-02 8.12e+03 1.18e+01
  ... (remaining 27982 not shown)

  Histogram of bond angle deviations from ideal:
       95.88 -   104.27: 433
      104.27 -   112.67: 14341
      112.67 -   121.07: 14744
      121.07 -   129.47: 8435
      129.47 -   137.87: 120
  Bond angle restraints: 38073
  Sorted by residual:
  angle pdb=" CA  PRO D 112 "
        pdb=" N   PRO D 112 "
        pdb=" CD  PRO D 112 "
      ideal   model   delta    sigma   weight residual
     112.00   99.50   12.50 1.40e+00 5.10e-01 7.97e+01
  angle pdb=" CA  PRO E 112 "
        pdb=" N   PRO E 112 "
        pdb=" CD  PRO E 112 "
      ideal   model   delta    sigma   weight residual
     112.00   99.58   12.42 1.40e+00 5.10e-01 7.87e+01
  angle pdb=" N   ILE E  75 "
        pdb=" CA  ILE E  75 "
        pdb=" C   ILE E  75 "
      ideal   model   delta    sigma   weight residual
     113.20  105.05    8.15 9.60e-01 1.09e+00 7.20e+01
  angle pdb=" N   VAL A 826 "
        pdb=" CA  VAL A 826 "
        pdb=" C   VAL A 826 "
      ideal   model   delta    sigma   weight residual
     112.29  105.56    6.73 9.40e-01 1.13e+00 5.13e+01
  angle pdb=" C   PRO G  15 "
        pdb=" CA  PRO G  15 "
        pdb=" CB  PRO G  15 "
      ideal   model   delta    sigma   weight residual
     112.64  100.60   12.04 1.74e+00 3.30e-01 4.79e+01
  ... (remaining 38068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 15405
       17.94 -    35.88: 1281
       35.88 -    53.82: 215
       53.82 -    71.76: 66
       71.76 -    89.70: 24
  Dihedral angle restraints: 16991
    sinusoidal: 6930
      harmonic: 10061
  Sorted by residual:
  dihedral pdb=" CB  CYS B1032 "
           pdb=" SG  CYS B1032 "
           pdb=" SG  CYS B1043 "
           pdb=" CB  CYS B1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.32  -84.32     1      1.00e+01 1.00e-02 8.65e+01
  dihedral pdb=" CB  CYS A 662 "
           pdb=" SG  CYS A 662 "
           pdb=" SG  CYS A 671 "
           pdb=" CB  CYS A 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.65   75.65     1      1.00e+01 1.00e-02 7.22e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  92 "
           pdb=" CB  CYS E  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.07  -75.07     1      1.00e+01 1.00e-02 7.13e+01
  ... (remaining 16988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.158: 4268
       0.158 -    0.317: 116
       0.317 -    0.475: 9
       0.475 -    0.634: 5
       0.634 -    0.792: 2
  Chirality restraints: 4400
  Sorted by residual:
  chirality pdb=" C1  NAG C1301 "
            pdb=" ND2 ASN A 282 "
            pdb=" C2  NAG C1301 "
            pdb=" O5  NAG C1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.61   -0.79 2.00e-01 2.50e+01 1.57e+01
  chirality pdb=" C1  NAG A1303 "
            pdb=" ND2 ASN A 331 "
            pdb=" C2  NAG A1303 "
            pdb=" O5  NAG A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.66   -0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A  61 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.81   -0.59 2.00e-01 2.50e+01 8.82e+00
  ... (remaining 4397 not shown)

  Planarity restraints: 4917
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C1310 "    0.320 2.00e-02 2.50e+03   2.80e-01 9.77e+02
        pdb=" C7  NAG C1310 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  NAG C1310 "    0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG C1310 "   -0.500 2.00e-02 2.50e+03
        pdb=" O7  NAG C1310 "    0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 234 "   -0.013 2.00e-02 2.50e+03   6.35e-02 5.03e+01
        pdb=" CG  ASN C 234 "    0.091 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 234 "   -0.075 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 234 "    0.053 2.00e-02 2.50e+03
        pdb=" C1  NAG C1303 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 234 "   -0.023 2.00e-02 2.50e+03   4.59e-02 2.11e+01
        pdb=" CG  ASN C 234 "    0.079 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 234 "   -0.030 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 234 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 4914 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 1647
        2.72 -     3.26: 27978
        3.26 -     3.81: 46939
        3.81 -     4.35: 56702
        4.35 -     4.90: 91334
  Nonbonded interactions: 224600
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 125 "
            pdb=" O6  NAG A1302 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   GLN A 804 "
            pdb=" OG  SER A 816 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OD1 ASN B 370 "
            pdb=" OG1 THR E 100B"
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR A 756 "
            pdb=" OD1 ASP A 994 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OE1 GLN G   6 "
            pdb=" OG1 THR G 103 "
     model   vdw
     2.241 3.040
  ... (remaining 224595 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 27 through 1147 or resid 1301 through 1308))
  selection = chain 'B'
  selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1308))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.810
  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:          1.140
  Check model and map are aligned:         0.200
  Set scattering table:                    0.270
  Process input model:                     68.530
  Find NCS groups from input model:        1.490
  Set up NCS constraints:                  0.150
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   78.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
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      :  0.006   0.095  27987  Z= 0.424
  Angle     :  1.130  21.570  38073  Z= 0.639
  Chirality :  0.071   0.792   4400
  Planarity :  0.009   0.280   4890
  Dihedral  : 13.704  89.695  10404
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.05 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.03 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.13), residues: 3420
  helix: -1.66 (0.18), residues: 622
  sheet: -1.41 (0.22), residues: 493
  loop : -1.87 (0.12), residues: 2305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP E  47 
 HIS   0.017   0.002   HIS A  49 
 PHE   0.054   0.003   PHE A 201 
 TYR   0.043   0.003   TYR C 917 
 ARG   0.015   0.001   ARG A 905 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 329
  time to evaluate  : 2.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 PHE cc_start: 0.5971 (m-10) cc_final: 0.5603 (m-80)
REVERT: A  515 PHE cc_start: 0.8932 (m-80) cc_final: 0.8574 (m-80)
REVERT: A  562 PHE cc_start: 0.8679 (t80) cc_final: 0.8236 (t80)
REVERT: A  960 ASN cc_start: 0.8586 (t0) cc_final: 0.8374 (t0)
REVERT: A 1095 PHE cc_start: 0.7622 (m-10) cc_final: 0.7277 (m-10)
REVERT: B  864 LEU cc_start: 0.7323 (tt) cc_final: 0.6518 (mm)
REVERT: B  976 VAL cc_start: 0.8844 (t) cc_final: 0.8284 (t)
REVERT: C  271 GLN cc_start: 0.5800 (mm-40) cc_final: 0.5508 (mm-40)
REVERT: C  336 CYS cc_start: 0.2353 (OUTLIER) cc_final: 0.1802 (t)
REVERT: E   51 MET cc_start: 0.5989 (tpt) cc_final: 0.5537 (tpt)
REVERT: E  100 MET cc_start: 0.8810 (tpt) cc_final: 0.8606 (tpt)
REVERT: G   32 ASP cc_start: 0.4368 (m-30) cc_final: 0.3951 (t0)
  outliers start: 8
  outliers final: 1
  residues processed: 336
  average time/residue: 0.3583
  time to fit residues: 195.9617
Evaluate side-chains
  226 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 224
  time to evaluate  : 2.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  358 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 290 optimal weight:    1.9990
   chunk 260 optimal weight:    3.9990
   chunk 144 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 175 optimal weight:    0.9990
   chunk 139 optimal weight:    0.0370
   chunk 269 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 163 optimal weight:    0.5980
   chunk 200 optimal weight:   10.0000
   chunk 312 optimal weight:    7.9990
   overall best weight:    1.3264

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 HIS
A 926 GLN
A1054 GLN
A1135 ASN
B  49 HIS
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
B 644 GLN
** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 360 ASN
C 774 GLN
** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
D  72 ASN
D 105 GLN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  27987  Z= 0.214
  Angle     :  0.693  11.927  38073  Z= 0.357
  Chirality :  0.049   0.487   4400
  Planarity :  0.005   0.060   4890
  Dihedral  :  8.293  59.963   4310
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.14 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.13), residues: 3420
  helix: -1.18 (0.19), residues: 636
  sheet: -1.25 (0.23), residues: 476
  loop : -1.79 (0.12), residues: 2308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  47 
 HIS   0.006   0.001   HIS C1048 
 PHE   0.026   0.002   PHE C 338 
 TYR   0.018   0.002   TYR B 200 
 ARG   0.006   0.001   ARG B1091 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 253
  time to evaluate  : 3.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLU cc_start: 0.7864 (pm20) cc_final: 0.7508 (pm20)
REVERT: A  562 PHE cc_start: 0.8676 (t80) cc_final: 0.8407 (t80)
REVERT: A  824 ASN cc_start: 0.8231 (t0) cc_final: 0.7867 (t0)
REVERT: A  960 ASN cc_start: 0.8730 (t0) cc_final: 0.8480 (t0)
REVERT: A  978 ASN cc_start: 0.8377 (m-40) cc_final: 0.8014 (p0)
REVERT: A 1037 SER cc_start: 0.8646 (t) cc_final: 0.8434 (m)
REVERT: A 1095 PHE cc_start: 0.7791 (m-10) cc_final: 0.7530 (m-10)
REVERT: B  201 PHE cc_start: 0.6958 (t80) cc_final: 0.6590 (t80)
REVERT: B  402 ILE cc_start: 0.3426 (tp) cc_final: 0.3157 (tp)
REVERT: C  336 CYS cc_start: 0.2339 (OUTLIER) cc_final: 0.1654 (t)
REVERT: C  346 ARG cc_start: 0.4414 (tpt-90) cc_final: 0.3963 (tpt-90)
REVERT: C  360 ASN cc_start: 0.4458 (OUTLIER) cc_final: 0.2857 (t0)
REVERT: D   69 MET cc_start: 0.7043 (tpp) cc_final: 0.6770 (tpt)
REVERT: E   51 MET cc_start: 0.5879 (tpt) cc_final: 0.5573 (tpt)
REVERT: E   69 MET cc_start: 0.3754 (mpp) cc_final: 0.3163 (mmp)
REVERT: G   32 ASP cc_start: 0.4361 (m-30) cc_final: 0.3699 (t0)
REVERT: G   45 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7536 (mmtp)
REVERT: G   47 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8035 (pp)
  outliers start: 39
  outliers final: 20
  residues processed: 280
  average time/residue: 0.3555
  time to fit residues: 166.9266
Evaluate side-chains
  229 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 3.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1051 SER
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  360 ASN
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  768 THR
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   47 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 173 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 259 optimal weight:    0.7980
   chunk 212 optimal weight:   10.0000
   chunk 86 optimal weight:    0.6980
   chunk 312 optimal weight:    8.9990
   chunk 338 optimal weight:    4.9990
   chunk 278 optimal weight:    4.9990
   chunk 310 optimal weight:   20.0000
   chunk 106 optimal weight:    0.0470
   chunk 251 optimal weight:    4.9990
   overall best weight:    2.3082

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  53 ASN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  27987  Z= 0.260
  Angle     :  0.672   9.543  38073  Z= 0.347
  Chirality :  0.048   0.451   4400
  Planarity :  0.005   0.057   4890
  Dihedral  :  7.685  58.720   4310
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.70 %
    Favored  : 85.17 %
  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: -2.22 (0.13), residues: 3420
  helix: -0.90 (0.19), residues: 639
  sheet: -1.30 (0.23), residues: 458
  loop : -1.77 (0.12), residues: 2323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 103 
 HIS   0.008   0.001   HIS C1048 
 PHE   0.020   0.002   PHE B 201 
 TYR   0.027   0.002   TYR D 100E
 ARG   0.005   0.001   ARG A 357 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 229
  time to evaluate  : 3.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 ARG cc_start: 0.5815 (OUTLIER) cc_final: 0.5272 (ttt90)
REVERT: A  516 GLU cc_start: 0.7955 (pm20) cc_final: 0.7615 (pm20)
REVERT: A  562 PHE cc_start: 0.8664 (t80) cc_final: 0.8422 (t80)
REVERT: A  824 ASN cc_start: 0.8270 (t0) cc_final: 0.7945 (t0)
REVERT: A  960 ASN cc_start: 0.8729 (t0) cc_final: 0.8485 (t0)
REVERT: A 1095 PHE cc_start: 0.7799 (m-10) cc_final: 0.7457 (m-10)
REVERT: B  201 PHE cc_start: 0.7235 (t80) cc_final: 0.7001 (t80)
REVERT: B  402 ILE cc_start: 0.3772 (tp) cc_final: 0.3492 (tp)
REVERT: B  697 MET cc_start: 0.7487 (ppp) cc_final: 0.7048 (ppp)
REVERT: B  764 ASN cc_start: 0.8741 (t0) cc_final: 0.8385 (t0)
REVERT: B  979 ASP cc_start: 0.8243 (m-30) cc_final: 0.7680 (t0)
REVERT: C  200 TYR cc_start: 0.7923 (m-80) cc_final: 0.7461 (m-80)
REVERT: C  336 CYS cc_start: 0.1963 (OUTLIER) cc_final: 0.1431 (t)
REVERT: D   69 MET cc_start: 0.7018 (tpp) cc_final: 0.6738 (tpt)
REVERT: G   32 ASP cc_start: 0.4309 (m-30) cc_final: 0.3856 (t0)
REVERT: G   45 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7574 (mmtp)
REVERT: G   47 LEU cc_start: 0.8525 (mt) cc_final: 0.8118 (pp)
  outliers start: 64
  outliers final: 33
  residues processed: 276
  average time/residue: 0.3373
  time to fit residues: 158.2183
Evaluate side-chains
  237 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 202
  time to evaluate  : 3.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1051 SER
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  730 SER
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  497 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  900 MET
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1050 MET
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 309 optimal weight:    0.9990
   chunk 235 optimal weight:    9.9990
   chunk 162 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 149 optimal weight:    6.9990
   chunk 210 optimal weight:    9.9990
   chunk 314 optimal weight:    8.9990
   chunk 332 optimal weight:   30.0000
   chunk 164 optimal weight:    9.9990
   chunk 297 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
A 448 ASN
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 804 GLN
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN
B 501 ASN
B 519 HIS
** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 GLN
C 901 GLN
C 926 GLN
C 949 GLN
C1054 GLN
** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  27987  Z= 0.320
  Angle     :  0.698  13.580  38073  Z= 0.362
  Chirality :  0.048   0.478   4400
  Planarity :  0.005   0.055   4890
  Dihedral  :  7.518  58.908   4310
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.43 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.13), residues: 3420
  helix: -0.87 (0.19), residues: 637
  sheet: -1.38 (0.23), residues: 456
  loop : -1.80 (0.12), residues: 2327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 353 
 HIS   0.010   0.002   HIS B1048 
 PHE   0.022   0.002   PHE B 927 
 TYR   0.023   0.002   TYR C 266 
 ARG   0.007   0.001   ARG B 237 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 103
    poor density    : 225
  time to evaluate  : 3.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 GLN cc_start: -0.1276 (OUTLIER) cc_final: -0.2123 (tt0)
REVERT: A  201 PHE cc_start: 0.7832 (m-80) cc_final: 0.7514 (m-10)
REVERT: A  509 ARG cc_start: 0.5621 (OUTLIER) cc_final: 0.5037 (tpt170)
REVERT: A  516 GLU cc_start: 0.8096 (pm20) cc_final: 0.7751 (pm20)
REVERT: A  562 PHE cc_start: 0.8571 (t80) cc_final: 0.8287 (t80)
REVERT: A  824 ASN cc_start: 0.8231 (t0) cc_final: 0.7938 (t0)
REVERT: A  950 ASP cc_start: 0.8357 (p0) cc_final: 0.7792 (p0)
REVERT: A  984 LEU cc_start: 0.6342 (tp) cc_final: 0.6064 (tp)
REVERT: A 1095 PHE cc_start: 0.7894 (m-10) cc_final: 0.7496 (m-10)
REVERT: B  697 MET cc_start: 0.7365 (ppp) cc_final: 0.7078 (ppp)
REVERT: B  764 ASN cc_start: 0.8791 (t0) cc_final: 0.8440 (t0)
REVERT: B  765 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8555 (ttm110)
REVERT: B  979 ASP cc_start: 0.8331 (m-30) cc_final: 0.7883 (t0)
REVERT: D   69 MET cc_start: 0.7174 (tpp) cc_final: 0.6749 (tpt)
REVERT: E   69 MET cc_start: 0.3580 (mpp) cc_final: 0.3089 (mmp)
REVERT: G   32 ASP cc_start: 0.4143 (m-30) cc_final: 0.3614 (t70)
REVERT: G   36 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5222 (m-80)
REVERT: G   45 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7647 (mmtm)
REVERT: G   47 LEU cc_start: 0.8660 (mt) cc_final: 0.8322 (pp)
  outliers start: 103
  outliers final: 53
  residues processed: 305
  average time/residue: 0.3429
  time to fit residues: 178.2324
Evaluate side-chains
  247 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 191
  time to evaluate  : 3.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  730 SER
Chi-restraints excluded: chain B residue  736 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  870 ILE
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  761 THR
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  768 THR
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1050 MET
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   36 TYR
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 276 optimal weight:    0.7980
   chunk 188 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 247 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   chunk 283 optimal weight:    0.7980
   chunk 229 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 169 optimal weight:    0.9990
   chunk 298 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 448 ASN
A 787 GLN
A 895 GLN
B  61 ASN
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
B 762 GLN
B 965 GLN
B1101 HIS
C 901 GLN
D   3 GLN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  27987  Z= 0.189
  Angle     :  0.643  12.648  38073  Z= 0.327
  Chirality :  0.048   0.452   4400
  Planarity :  0.004   0.053   4890
  Dihedral  :  7.214  59.755   4309
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.19 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.14), residues: 3420
  helix: -0.75 (0.19), residues: 636
  sheet: -1.18 (0.23), residues: 470
  loop : -1.70 (0.13), residues: 2314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  47 
 HIS   0.008   0.001   HIS B1048 
 PHE   0.033   0.002   PHE C 497 
 TYR   0.023   0.001   TYR C 365 
 ARG   0.005   0.000   ARG A 509 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 87
    poor density    : 233
  time to evaluate  : 3.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.7840 (m-10) cc_final: 0.7127 (m-10)
REVERT: A  115 GLN cc_start: -0.1372 (OUTLIER) cc_final: -0.2139 (tt0)
REVERT: A  201 PHE cc_start: 0.7628 (m-80) cc_final: 0.7327 (m-10)
REVERT: A  275 PHE cc_start: 0.6131 (m-80) cc_final: 0.5271 (m-80)
REVERT: A  516 GLU cc_start: 0.8056 (pm20) cc_final: 0.7734 (pm20)
REVERT: A  562 PHE cc_start: 0.8319 (t80) cc_final: 0.8060 (t80)
REVERT: A  824 ASN cc_start: 0.8166 (t0) cc_final: 0.7890 (t0)
REVERT: A  950 ASP cc_start: 0.8189 (p0) cc_final: 0.7932 (p0)
REVERT: A 1095 PHE cc_start: 0.7842 (m-10) cc_final: 0.7496 (m-10)
REVERT: B  697 MET cc_start: 0.7203 (ppp) cc_final: 0.6963 (ppp)
REVERT: B  762 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8738 (pm20)
REVERT: B  763 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8750 (mm)
REVERT: B  764 ASN cc_start: 0.8746 (t0) cc_final: 0.8368 (t0)
REVERT: B  869 MET cc_start: 0.6940 (ptt) cc_final: 0.6590 (ptt)
REVERT: B  979 ASP cc_start: 0.8220 (m-30) cc_final: 0.7962 (t0)
REVERT: B  984 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (mm)
REVERT: C  200 TYR cc_start: 0.8103 (m-80) cc_final: 0.7452 (m-80)
REVERT: C  346 ARG cc_start: 0.4416 (tpt-90) cc_final: 0.3917 (tpt170)
REVERT: C  396 TYR cc_start: 0.3327 (OUTLIER) cc_final: 0.3083 (m-80)
REVERT: C  515 PHE cc_start: 0.0192 (OUTLIER) cc_final: -0.0119 (p90)
REVERT: C  802 PHE cc_start: 0.8221 (m-10) cc_final: 0.7897 (m-80)
REVERT: D   69 MET cc_start: 0.7103 (tpp) cc_final: 0.6630 (tpt)
REVERT: D   91 PHE cc_start: 0.5870 (OUTLIER) cc_final: 0.5475 (t80)
REVERT: E   69 MET cc_start: 0.3443 (mpp) cc_final: 0.2914 (mmp)
REVERT: G   32 ASP cc_start: 0.3925 (m-30) cc_final: 0.3475 (t70)
  outliers start: 87
  outliers final: 51
  residues processed: 299
  average time/residue: 0.3349
  time to fit residues: 169.5188
Evaluate side-chains
  268 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 210
  time to evaluate  : 2.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 GLN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  915 VAL
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1029 MET
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  859 THR
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue  957 GLN
Chi-restraints excluded: chain C residue 1050 MET
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 299 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 195 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 332 optimal weight:   20.0000
   chunk 276 optimal weight:    5.9990
   chunk 154 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0270
   chunk 174 optimal weight:    6.9990
   overall best weight:    0.9240

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

Flipped N/Q/H residues before XYZ refinement:
** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1011 GLN
B  61 ASN
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
B 901 GLN
D   3 GLN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  27987  Z= 0.192
  Angle     :  0.642  13.490  38073  Z= 0.327
  Chirality :  0.047   0.436   4400
  Planarity :  0.004   0.052   4890
  Dihedral  :  7.064  59.626   4309
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.19 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.14), residues: 3420
  helix: -0.83 (0.19), residues: 647
  sheet: -1.23 (0.23), residues: 486
  loop : -1.66 (0.13), residues: 2287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G  35 
 HIS   0.008   0.001   HIS C1048 
 PHE   0.027   0.001   PHE C 497 
 TYR   0.019   0.001   TYR B 873 
 ARG   0.005   0.000   ARG A 509 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 93
    poor density    : 232
  time to evaluate  : 3.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.7915 (m-10) cc_final: 0.7407 (m-10)
REVERT: A  115 GLN cc_start: -0.1337 (OUTLIER) cc_final: -0.2090 (tt0)
REVERT: A  201 PHE cc_start: 0.7592 (m-80) cc_final: 0.7286 (m-10)
REVERT: A  275 PHE cc_start: 0.6262 (m-80) cc_final: 0.5423 (m-80)
REVERT: A  516 GLU cc_start: 0.8037 (pm20) cc_final: 0.7736 (pm20)
REVERT: A  824 ASN cc_start: 0.8156 (t0) cc_final: 0.7898 (t0)
REVERT: A 1095 PHE cc_start: 0.7823 (m-10) cc_final: 0.7468 (m-10)
REVERT: A 1125 ASN cc_start: 0.7759 (p0) cc_final: 0.7314 (t0)
REVERT: B  697 MET cc_start: 0.7141 (ppp) cc_final: 0.6932 (ppp)
REVERT: B  764 ASN cc_start: 0.8702 (t0) cc_final: 0.8296 (t0)
REVERT: B  979 ASP cc_start: 0.8206 (m-30) cc_final: 0.7988 (t0)
REVERT: B  984 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8054 (mm)
REVERT: C  346 ARG cc_start: 0.4406 (tpt-90) cc_final: 0.3911 (tpt170)
REVERT: C  396 TYR cc_start: 0.3238 (OUTLIER) cc_final: 0.2975 (m-80)
REVERT: C  515 PHE cc_start: 0.0057 (OUTLIER) cc_final: -0.0254 (p90)
REVERT: C  802 PHE cc_start: 0.8237 (m-10) cc_final: 0.7926 (m-80)
REVERT: D   69 MET cc_start: 0.7169 (tpp) cc_final: 0.6873 (tpt)
REVERT: D   91 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5465 (t80)
REVERT: E   69 MET cc_start: 0.3308 (mpp) cc_final: 0.2169 (tpt)
REVERT: G   32 ASP cc_start: 0.3880 (m-30) cc_final: 0.3461 (t0)
REVERT: G   47 LEU cc_start: 0.8508 (mt) cc_final: 0.8092 (pp)
  outliers start: 93
  outliers final: 54
  residues processed: 305
  average time/residue: 0.3287
  time to fit residues: 171.3829
Evaluate side-chains
  267 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 208
  time to evaluate  : 2.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  951 VAL
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  438 SER
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  767 LEU
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  859 THR
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue  957 GLN
Chi-restraints excluded: chain C residue 1032 CYS
Chi-restraints excluded: chain C residue 1050 MET
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 320 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 189 optimal weight:    5.9990
   chunk 243 optimal weight:    2.9990
   chunk 188 optimal weight:    0.8980
   chunk 280 optimal weight:    1.9990
   chunk 185 optimal weight:    0.9980
   chunk 331 optimal weight:    0.5980
   chunk 207 optimal weight:    4.9990
   chunk 202 optimal weight:    4.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B  61 ASN
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
C 784 GLN
** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  27987  Z= 0.210
  Angle     :  0.639   9.630  38073  Z= 0.326
  Chirality :  0.047   0.440   4400
  Planarity :  0.004   0.050   4890
  Dihedral  :  6.973  59.981   4309
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.18 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.14), residues: 3420
  helix: -0.77 (0.19), residues: 641
  sheet: -1.09 (0.24), residues: 478
  loop : -1.67 (0.13), residues: 2301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 353 
 HIS   0.015   0.001   HIS B1048 
 PHE   0.038   0.002   PHE A 562 
 TYR   0.018   0.001   TYR C 365 
 ARG   0.005   0.000   ARG A 509 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 90
    poor density    : 220
  time to evaluate  : 3.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 GLN cc_start: -0.1105 (OUTLIER) cc_final: -0.1887 (tt0)
REVERT: A  201 PHE cc_start: 0.7631 (m-80) cc_final: 0.7311 (m-10)
REVERT: A  516 GLU cc_start: 0.8029 (pm20) cc_final: 0.7733 (pm20)
REVERT: A  824 ASN cc_start: 0.8187 (t0) cc_final: 0.7933 (t0)
REVERT: A  950 ASP cc_start: 0.8297 (p0) cc_final: 0.8042 (p0)
REVERT: A 1095 PHE cc_start: 0.7840 (m-10) cc_final: 0.7417 (m-10)
REVERT: A 1125 ASN cc_start: 0.7770 (p0) cc_final: 0.7351 (t0)
REVERT: B  764 ASN cc_start: 0.8740 (t0) cc_final: 0.8401 (t0)
REVERT: B  765 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8478 (ttm110)
REVERT: B  900 MET cc_start: 0.7025 (mmt) cc_final: 0.5913 (mmt)
REVERT: B  984 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8078 (mm)
REVERT: C  271 GLN cc_start: 0.6242 (mm-40) cc_final: 0.6001 (mm-40)
REVERT: C  346 ARG cc_start: 0.4369 (tpt-90) cc_final: 0.3821 (tpt170)
REVERT: C  396 TYR cc_start: 0.3298 (OUTLIER) cc_final: 0.3040 (m-80)
REVERT: C  802 PHE cc_start: 0.8313 (m-10) cc_final: 0.8009 (m-80)
REVERT: D   69 MET cc_start: 0.7253 (tpp) cc_final: 0.6962 (tpt)
REVERT: D   91 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5584 (t80)
REVERT: E   69 MET cc_start: 0.3420 (mpp) cc_final: 0.2310 (tpt)
REVERT: G   32 ASP cc_start: 0.3933 (m-30) cc_final: 0.3530 (t0)
REVERT: G   36 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.5213 (m-80)
REVERT: G   45 LYS cc_start: 0.8043 (mppt) cc_final: 0.7811 (mppt)
REVERT: G   47 LEU cc_start: 0.8507 (mt) cc_final: 0.8127 (pp)
  outliers start: 90
  outliers final: 62
  residues processed: 288
  average time/residue: 0.3391
  time to fit residues: 165.4475
Evaluate side-chains
  270 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 203
  time to evaluate  : 3.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  761 THR
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  438 SER
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  736 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  957 GLN
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1029 MET
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  762 GLN
Chi-restraints excluded: chain C residue  767 LEU
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  859 THR
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1032 CYS
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   36 TYR
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 205 optimal weight:   10.0000
   chunk 132 optimal weight:    0.0270
   chunk 198 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 210 optimal weight:    7.9990
   chunk 225 optimal weight:    5.9990
   chunk 163 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 260 optimal weight:    0.0060
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
B  61 ASN
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
B 762 GLN
B 895 GLN
B1088 HIS
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  27987  Z= 0.171
  Angle     :  0.631  11.642  38073  Z= 0.321
  Chirality :  0.047   0.421   4400
  Planarity :  0.004   0.052   4890
  Dihedral  :  6.817  59.956   4309
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.95 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.14), residues: 3420
  helix: -0.82 (0.19), residues: 643
  sheet: -1.01 (0.24), residues: 468
  loop : -1.60 (0.13), residues: 2309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  47 
 HIS   0.008   0.001   HIS C1048 
 PHE   0.020   0.001   PHE C 497 
 TYR   0.019   0.001   TYR C 508 
 ARG   0.007   0.000   ARG E  66 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 234
  time to evaluate  : 3.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 GLN cc_start: -0.1019 (OUTLIER) cc_final: -0.1814 (tt0)
REVERT: A  135 PHE cc_start: 0.7358 (m-10) cc_final: 0.7120 (m-10)
REVERT: A  516 GLU cc_start: 0.7871 (pm20) cc_final: 0.7655 (pm20)
REVERT: A  824 ASN cc_start: 0.8081 (t0) cc_final: 0.7865 (t0)
REVERT: A  988 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8460 (mp0)
REVERT: A 1095 PHE cc_start: 0.7750 (m-10) cc_final: 0.7338 (m-10)
REVERT: A 1125 ASN cc_start: 0.7679 (p0) cc_final: 0.7296 (t0)
REVERT: B  359 SER cc_start: 0.7658 (t) cc_final: 0.7430 (p)
REVERT: B  764 ASN cc_start: 0.8698 (t0) cc_final: 0.8342 (t0)
REVERT: B  765 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8413 (ttm110)
REVERT: B  900 MET cc_start: 0.7044 (mmt) cc_final: 0.5849 (mmt)
REVERT: B  984 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8033 (mm)
REVERT: C  346 ARG cc_start: 0.4346 (tpt-90) cc_final: 0.3790 (tpt170)
REVERT: C  357 ARG cc_start: 0.4387 (OUTLIER) cc_final: 0.3802 (ptp-170)
REVERT: C  396 TYR cc_start: 0.3324 (OUTLIER) cc_final: 0.3053 (m-10)
REVERT: C  450 ASN cc_start: 0.6069 (p0) cc_final: 0.5151 (t0)
REVERT: C  802 PHE cc_start: 0.8188 (m-10) cc_final: 0.7883 (m-80)
REVERT: D   51 MET cc_start: 0.8304 (tpp) cc_final: 0.7579 (tpp)
REVERT: D   91 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5732 (t80)
REVERT: E   69 MET cc_start: 0.3105 (mpp) cc_final: 0.2763 (tpp)
REVERT: G   36 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5183 (m-80)
REVERT: G   45 LYS cc_start: 0.8081 (mppt) cc_final: 0.7831 (mppt)
REVERT: G   47 LEU cc_start: 0.8548 (mt) cc_final: 0.8184 (pp)
  outliers start: 83
  outliers final: 60
  residues processed: 296
  average time/residue: 0.3477
  time to fit residues: 174.3705
Evaluate side-chains
  278 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 212
  time to evaluate  : 3.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  954 GLN
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  438 SER
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  571 ASP
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  736 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 GLN
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  957 GLN
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain B residue 1139 ASP
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  357 ARG
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  767 LEU
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  909 ILE
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1032 CYS
Chi-restraints excluded: chain C residue 1092 GLU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  100 TYR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   36 TYR
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 301 optimal weight:    5.9990
   chunk 317 optimal weight:    7.9990
   chunk 289 optimal weight:    5.9990
   chunk 308 optimal weight:   10.0000
   chunk 185 optimal weight:    0.8980
   chunk 134 optimal weight:   10.0000
   chunk 242 optimal weight:   20.0000
   chunk 94 optimal weight:    0.7980
   chunk 279 optimal weight:    8.9990
   chunk 292 optimal weight:    1.9990
   chunk 307 optimal weight:    4.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 GLN
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
C 901 GLN
** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
E  56 ASN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  27987  Z= 0.296
  Angle     :  0.690  12.083  38073  Z= 0.356
  Chirality :  0.048   0.456   4400
  Planarity :  0.005   0.048   4890
  Dihedral  :  6.944  59.613   4309
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.75 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.71 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.14), residues: 3420
  helix: -0.84 (0.19), residues: 645
  sheet: -1.08 (0.23), residues: 488
  loop : -1.67 (0.13), residues: 2287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1102 
 HIS   0.014   0.001   HIS B1048 
 PHE   0.023   0.002   PHE C 497 
 TYR   0.021   0.002   TYR B 873 
 ARG   0.008   0.001   ARG B 983 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 208
  time to evaluate  : 3.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.7916 (m-10) cc_final: 0.7690 (m-10)
REVERT: A  115 GLN cc_start: -0.0934 (OUTLIER) cc_final: -0.1695 (tt0)
REVERT: A  516 GLU cc_start: 0.7958 (pm20) cc_final: 0.7552 (pm20)
REVERT: A  824 ASN cc_start: 0.8193 (t0) cc_final: 0.7919 (t0)
REVERT: A 1095 PHE cc_start: 0.7867 (m-10) cc_final: 0.7455 (m-10)
REVERT: A 1125 ASN cc_start: 0.7700 (p0) cc_final: 0.7400 (t0)
REVERT: B  764 ASN cc_start: 0.8801 (t0) cc_final: 0.8497 (t0)
REVERT: B  765 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8583 (ttm110)
REVERT: B  900 MET cc_start: 0.7130 (mmt) cc_final: 0.5997 (mmt)
REVERT: B  984 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8138 (mm)
REVERT: C  346 ARG cc_start: 0.4300 (tpt-90) cc_final: 0.3759 (tpt170)
REVERT: C  357 ARG cc_start: 0.4282 (OUTLIER) cc_final: 0.3705 (ptp-170)
REVERT: C  396 TYR cc_start: 0.3487 (OUTLIER) cc_final: 0.3195 (m-10)
REVERT: C  802 PHE cc_start: 0.8413 (m-10) cc_final: 0.8100 (m-80)
REVERT: D   91 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5673 (t80)
REVERT: E   69 MET cc_start: 0.3700 (mpp) cc_final: 0.3332 (tpp)
REVERT: G   36 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.5299 (m-80)
REVERT: G   45 LYS cc_start: 0.8064 (mppt) cc_final: 0.7860 (mppt)
REVERT: G   47 LEU cc_start: 0.8451 (mt) cc_final: 0.8089 (pp)
  outliers start: 85
  outliers final: 65
  residues processed: 276
  average time/residue: 0.3465
  time to fit residues: 162.5414
Evaluate side-chains
  267 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 196
  time to evaluate  : 3.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  954 GLN
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  438 SER
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  730 SER
Chi-restraints excluded: chain B residue  736 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  761 THR
Chi-restraints excluded: chain B residue  767 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  870 ILE
Chi-restraints excluded: chain B residue  957 GLN
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  357 ARG
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  767 LEU
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  859 THR
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  900 MET
Chi-restraints excluded: chain C residue  909 ILE
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1034 LEU
Chi-restraints excluded: chain C residue 1122 VAL
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   36 TYR
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 202 optimal weight:    7.9990
   chunk 326 optimal weight:    5.9990
   chunk 199 optimal weight:    0.5980
   chunk 154 optimal weight:    6.9990
   chunk 227 optimal weight:    0.9990
   chunk 342 optimal weight:    3.9990
   chunk 315 optimal weight:   20.0000
   chunk 272 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 210 optimal weight:    9.9990
   chunk 167 optimal weight:    9.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
B1005 GLN
C 448 ASN
C 450 ASN
C 901 GLN
** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
E  56 ASN
F  27BASN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  27987  Z= 0.225
  Angle     :  0.663  12.315  38073  Z= 0.338
  Chirality :  0.047   0.442   4400
  Planarity :  0.004   0.051   4890
  Dihedral  :  6.850  59.953   4309
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.73 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.38 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.14), residues: 3420
  helix: -0.75 (0.20), residues: 647
  sheet: -1.02 (0.24), residues: 482
  loop : -1.65 (0.13), residues: 2291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  47 
 HIS   0.009   0.001   HIS C1048 
 PHE   0.070   0.002   PHE A 168 
 TYR   0.024   0.001   TYR C 365 
 ARG   0.007   0.000   ARG B 983 

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

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

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6840 Ramachandran restraints generated.
    3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 202
  time to evaluate  : 2.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 GLN cc_start: -0.0927 (OUTLIER) cc_final: -0.1714 (tt0)
REVERT: A  516 GLU cc_start: 0.7860 (pm20) cc_final: 0.7606 (pm20)
REVERT: A  824 ASN cc_start: 0.8178 (t0) cc_final: 0.7938 (t0)
REVERT: A  858 LEU cc_start: 0.8814 (pt) cc_final: 0.8528 (pp)
REVERT: A 1095 PHE cc_start: 0.7817 (m-10) cc_final: 0.7391 (m-10)
REVERT: A 1125 ASN cc_start: 0.7621 (p0) cc_final: 0.7388 (t0)
REVERT: B  764 ASN cc_start: 0.8814 (t0) cc_final: 0.8525 (t0)
REVERT: B  765 ARG cc_start: 0.8756 (ttm110) cc_final: 0.8392 (ttm110)
REVERT: B  900 MET cc_start: 0.7137 (mmt) cc_final: 0.5885 (mmt)
REVERT: B  984 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8111 (mm)
REVERT: C  346 ARG cc_start: 0.4293 (tpt-90) cc_final: 0.3745 (tpt170)
REVERT: C  357 ARG cc_start: 0.4241 (OUTLIER) cc_final: 0.3650 (ptp-170)
REVERT: C  396 TYR cc_start: 0.3545 (OUTLIER) cc_final: 0.3260 (m-10)
REVERT: C  904 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6528 (m-10)
REVERT: D   91 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.5686 (t80)
REVERT: E   69 MET cc_start: 0.3589 (mpp) cc_final: 0.3313 (tpp)
REVERT: G   36 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5324 (m-80)
REVERT: G   45 LYS cc_start: 0.8028 (mppt) cc_final: 0.7825 (mppt)
REVERT: G   47 LEU cc_start: 0.8464 (mt) cc_final: 0.8097 (pp)
  outliers start: 75
  outliers final: 66
  residues processed: 259
  average time/residue: 0.3410
  time to fit residues: 151.3462
Evaluate side-chains
  272 residues out of total 3008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 199
  time to evaluate  : 3.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  869 MET
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  954 GLN
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  438 SER
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  571 ASP
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  736 VAL
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  800 PHE
Chi-restraints excluded: chain B residue  826 VAL
Chi-restraints excluded: chain B residue  870 ILE
Chi-restraints excluded: chain B residue  957 GLN
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  984 LEU
Chi-restraints excluded: chain B residue  990 GLU
Chi-restraints excluded: chain B residue 1031 GLU
Chi-restraints excluded: chain B residue 1055 SER
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  357 ARG
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  767 LEU
Chi-restraints excluded: chain C residue  856 ASN
Chi-restraints excluded: chain C residue  859 THR
Chi-restraints excluded: chain C residue  873 TYR
Chi-restraints excluded: chain C residue  900 MET
Chi-restraints excluded: chain C residue  904 TYR
Chi-restraints excluded: chain C residue  909 ILE
Chi-restraints excluded: chain C residue  911 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Chi-restraints excluded: chain D residue    3 GLN
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   91 PHE
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   27 ASN
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue   36 TYR
Chi-restraints excluded: chain G residue   97 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 344
   random chunks:
   chunk 216 optimal weight:    0.0670
   chunk 290 optimal weight:    0.1980
   chunk 83 optimal weight:    1.9990
   chunk 251 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 273 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 280 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.2524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: