Starting phenix.real_space_refine
on Fri Aug  9 03:20:57 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/08_2024/8uk1_42342.cif"
  }
  resolution = 3.0
  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=  -0.000 sd=   0.065
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     115      5.16       5
     C   15810      2.51       5
     N    4073      2.21       5
     O    4808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   40": "OD1" <-> "OD2"
    Residue "A PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  170": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  578": "OD1" <-> "OD2"
    Residue "A TYR  612": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  988": "OE1" <-> "OE2"
    Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  369": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  571": "OD1" <-> "OD2"
    Residue "B ASP  574": "OD1" <-> "OD2"
    Residue "B ASP  578": "OD1" <-> "OD2"
    Residue "B ASP  586": "OD1" <-> "OD2"
    Residue "B GLU  619": "OE1" <-> "OE2"
    Residue "B ASP  745": "OD1" <-> "OD2"
    Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  420": "OD1" <-> "OD2"
    Residue "C TYR  501": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  543": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  574": "OD1" <-> "OD2"
    Residue "C ASP  745": "OD1" <-> "OD2"
    Residue "C TYR  873": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  904": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  950": "OD1" <-> "OD2"
    Residue "C ASP 1118": "OD1" <-> "OD2"
  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: 24806
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 8084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1036, 8084
          Classifications: {'peptide': 1036}
          Link IDs: {'PTRANS': 51, 'TRANS': 984}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 7988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1024, 7988
          Classifications: {'peptide': 1024}
          Link IDs: {'PTRANS': 51, 'TRANS': 972}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 8090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1037, 8090
          Classifications: {'peptide': 1037}
          Link IDs: {'PTRANS': 51, 'TRANS': 985}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "N"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 126
          Unusual residues: {'NAG': 9}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    Chain: "B"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 126
          Unusual residues: {'NAG': 9}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    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: 13.86, per 1000 atoms: 0.56
  Number of scatterers: 24806
  At special positions: 0
  Unit cell: (135, 129.6, 172.8, 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     115     16.00
     O    4808      8.00
     N    4073      7.00
     C   15810      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    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=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    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=2.03
    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 A 840 " - pdb=" SG  CYS A 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.02
    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=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    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=2.03
    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=2.03
    Simple disulfide: pdb=" SG  CYS B 840 " - pdb=" SG  CYS B 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03
    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=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    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=2.05
    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=2.03
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 840 " - pdb=" SG  CYS C 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG L   1 " - " NAG L   2 "
      " NAG M   1 " - " NAG M   2 "
      " NAG N   1 " - " NAG N   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 331 "
      " NAG A1303 " - " ASN A 343 "
      " NAG A1304 " - " ASN A 709 "
      " NAG A1305 " - " ASN A1074 "
      " NAG A1306 " - " ASN A1134 "
      " NAG A1307 " - " ASN A 282 "
      " NAG A1308 " - " ASN A 234 "
      " NAG A1309 " - " ASN A 616 "
      " NAG B1301 " - " ASN B  61 "
      " NAG B1302 " - " ASN B 282 "
      " NAG B1303 " - " ASN B 331 "
      " NAG B1304 " - " ASN B 343 "
      " NAG B1305 " - " ASN B1074 "
      " NAG B1306 " - " ASN B1134 "
      " NAG B1307 " - " ASN B 709 "
      " NAG B1308 " - " ASN B 616 "
      " NAG B1309 " - " ASN B 234 "
      " NAG C1301 " - " ASN C  61 "
      " NAG C1302 " - " ASN C 165 "
      " NAG C1303 " - " ASN C 282 "
      " NAG C1304 " - " ASN C 331 "
      " NAG C1305 " - " ASN C 343 "
      " NAG C1306 " - " ASN C 616 "
      " NAG C1307 " - " ASN C 709 "
      " NAG C1308 " - " ASN C1074 "
      " NAG C1309 " - " ASN C1134 "
      " NAG C1310 " - " ASN C 234 "
      " NAG D   1 " - " ASN A 801 "
      " NAG E   1 " - " ASN B 801 "
      " NAG F   1 " - " ASN A 717 "
      " NAG G   1 " - " ASN A1098 "
      " NAG I   1 " - " ASN B 717 "
      " NAG K   1 " - " ASN B1098 "
      " NAG L   1 " - " ASN C 717 "
      " NAG M   1 " - " ASN C 801 "
      " NAG N   1 " - " ASN C1098 "
  Time building additional restraints: 9.59
  Conformation dependent library (CDL) restraints added in 4.2 seconds
  

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5804

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 44 sheets defined
      25.2% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 367 through 372
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 737 through 743
    Processing helix  chain 'A' and resid 746 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 783
      removed outlier: 3.693A  pdb=" N   ASP A 775 " --> pdb=" O   ALA A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 826
      removed outlier: 3.566A  pdb=" N   VAL A 826 " --> pdb=" O   LEU A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 841
    Processing helix  chain 'A' and resid 848 through 856
    Processing helix  chain 'A' and resid 866 through 885
    Processing helix  chain 'A' and resid 886 through 890
    Processing helix  chain 'A' and resid 897 through 910
    Processing helix  chain 'A' and resid 912 through 918
      removed outlier: 4.096A  pdb=" N   LEU A 916 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 941
    Processing helix  chain 'A' and resid 945 through 965
      removed outlier: 3.748A  pdb=" N   LEU A 959 " --> pdb=" O   ASN A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 968
      No H-bonds generated for 'chain 'A' and resid 966 through 968'
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 985 through 1032
    Processing helix  chain 'A' and resid 1140 through 1146
      removed outlier: 3.615A  pdb=" N   GLU A1144 " --> pdb=" O   PRO A1140 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP A1146 " --> pdb=" O   GLN A1142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 386 through 389
    Processing helix  chain 'B' and resid 405 through 407
      No H-bonds generated for 'chain 'B' and resid 405 through 407'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 737 through 743
    Processing helix  chain 'B' and resid 746 through 754
    Processing helix  chain 'B' and resid 755 through 757
      No H-bonds generated for 'chain 'B' and resid 755 through 757'
    Processing helix  chain 'B' and resid 758 through 783
      removed outlier: 3.744A  pdb=" N   ASP B 775 " --> pdb=" O   ALA B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 826
      removed outlier: 3.724A  pdb=" N   VAL B 826 " --> pdb=" O   LEU B 822 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 836 through 842
    Processing helix  chain 'B' and resid 848 through 856
      removed outlier: 3.736A  pdb=" N   ALA B 852 " --> pdb=" O   ASP B 848 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASN B 856 " --> pdb=" O   ALA B 852 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 866 through 884
    Processing helix  chain 'B' and resid 886 through 891
      removed outlier: 3.777A  pdb=" N   ALA B 890 " --> pdb=" O   TRP B 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 910
    Processing helix  chain 'B' and resid 912 through 918
      removed outlier: 4.082A  pdb=" N   LEU B 916 " --> pdb=" O   THR B 912 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 919 through 941
    Processing helix  chain 'B' and resid 945 through 965
      removed outlier: 3.612A  pdb=" N   GLN B 949 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN B 955 " --> pdb=" O   VAL B 951 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 966 through 968
      No H-bonds generated for 'chain 'B' and resid 966 through 968'
    Processing helix  chain 'B' and resid 976 through 984
    Processing helix  chain 'B' and resid 985 through 1032
      removed outlier: 4.156A  pdb=" N   VAL B 991 " --> pdb=" O   VAL B 987 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLN B 992 " --> pdb=" O   GLU B 988 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1140 through 1146
      removed outlier: 3.867A  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 349 through 353
      removed outlier: 4.224A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 366
      No H-bonds generated for 'chain 'C' and resid 364 through 366'
    Processing helix  chain 'C' and resid 367 through 372
      removed outlier: 3.516A  pdb=" N   PHE C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 389
      removed outlier: 4.160A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'C' and resid 737 through 743
    Processing helix  chain 'C' and resid 746 through 757
      removed outlier: 3.642A  pdb=" N   GLY C 757 " --> pdb=" O   LEU C 753 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 758 through 783
      removed outlier: 4.080A  pdb=" N   GLN C 762 " --> pdb=" O   SER C 758 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 816 through 825
    Processing helix  chain 'C' and resid 848 through 856
    Processing helix  chain 'C' and resid 866 through 885
    Processing helix  chain 'C' and resid 897 through 910
    Processing helix  chain 'C' and resid 912 through 918
      removed outlier: 4.098A  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 965
    Processing helix  chain 'C' and resid 966 through 968
      No H-bonds generated for 'chain 'C' and resid 966 through 968'
    Processing helix  chain 'C' and resid 976 through 984
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 3.576A  pdb=" N   VAL C 991 " --> pdb=" O   VAL C 987 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1140 through 1146
      removed outlier: 3.933A  pdb=" N   GLU C1144 " --> pdb=" O   PRO C1140 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30
      removed outlier: 7.748A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.843A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR C 553 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55
      removed outlier: 3.903A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.626A  pdb=" N   LEU A  84 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319
      removed outlier: 5.303A  pdb=" N   ILE A 312 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   THR A 599 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   GLN A 314 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A 597 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER A 316 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY A 594 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.726A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.682A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543
      removed outlier: 5.389A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLY A 566 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   PHE A 565 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655
      removed outlier: 6.071A  pdb=" N   GLU A 654 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   THR A 696 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703
      removed outlier: 6.797A  pdb=" N   ALA A 701 " --> pdb=" O   ILE B 788 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715
      removed outlier: 3.866A  pdb=" N   ALA A1078 " --> pdb=" O   PHE A1095 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   PHE A1095 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728
      removed outlier: 6.078A  pdb=" N   TYR A1067 " --> pdb=" O   HIS A1048 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   HIS A1048 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736
      removed outlier: 4.563A  pdb=" N   LYS A 733 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122
    Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 29
      removed outlier: 3.665A  pdb=" N   TYR B 265 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 203 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55
      removed outlier: 4.402A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85
    Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319
      removed outlier: 5.394A  pdb=" N   ILE B 312 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   THR B 599 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   GLN B 314 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B 597 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 316 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY B 594 " --> pdb=" O   GLN B 613 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328
      removed outlier: 5.330A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   PHE B 565 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.725A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.593A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655
      removed outlier: 6.078A  pdb=" N   GLU B 654 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   THR B 696 " --> pdb=" O   GLU B 654 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715
      removed outlier: 3.963A  pdb=" N   ALA B1078 " --> pdb=" O   PHE B1095 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   PHE B1095 " --> pdb=" O   ALA B1078 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728
      removed outlier: 6.131A  pdb=" N   TYR B1067 " --> pdb=" O   HIS B1048 " (cutoff:3.500A)
      removed outlier: 5.816A  pdb=" N   HIS B1048 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736
      removed outlier: 4.579A  pdb=" N   LYS B 733 " --> pdb=" O   LEU B 861 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122
    Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.540A  pdb=" N   VAL C  62 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55
      removed outlier: 4.020A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85
      removed outlier: 3.713A  pdb=" N   LEU C  84 " --> pdb=" O   PHE C 238 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE C 238 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'C' and resid 118 through 121
    Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 314
      removed outlier: 3.681A  pdb=" N   GLY C 593 " --> pdb=" O   PHE C 318 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE C 318 " --> pdb=" O   GLY C 593 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314
      removed outlier: 3.797A  pdb=" N   GLY C 594 " --> pdb=" O   GLN C 613 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY C 648 " --> pdb=" O   THR C 645 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR C 645 " --> pdb=" O   GLY C 648 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358
      removed outlier: 4.247A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.577A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655
      removed outlier: 6.073A  pdb=" N   GLU C 654 " --> pdb=" O   ALA C 694 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   THR C 696 " --> pdb=" O   GLU C 654 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ALA C 672 " --> pdb=" O   PRO C 665 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713
      removed outlier: 3.707A  pdb=" N   ALA C1078 " --> pdb=" O   PHE C1095 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   PHE C1095 " --> pdb=" O   ALA C1078 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728
      removed outlier: 6.103A  pdb=" N   TYR C1067 " --> pdb=" O   HIS C1048 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   HIS C1048 " --> pdb=" O   TYR C1067 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736
      removed outlier: 4.602A  pdb=" N   LYS C 733 " --> pdb=" O   LEU C 861 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122

    984 hydrogen bonds defined for protein.
    2733 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 10.89

  Time building geometry restraints manager: 10.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 7891
        1.35 -     1.47: 6441
        1.47 -     1.60: 10876
        1.60 -     1.72: 0
        1.72 -     1.85: 142
  Bond restraints: 25350
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.62e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.30e+00
  bond pdb=" C1  NAG N   1 "
       pdb=" O5  NAG N   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.78e+00
  bond pdb=" C1  NAG C1306 "
       pdb=" O5  NAG C1306 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.69e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.62e+00
  ... (remaining 25345 not shown)

  Histogram of bond angle deviations from ideal:
       97.87 -   105.26: 470
      105.26 -   112.64: 13265
      112.64 -   120.03: 9056
      120.03 -   127.42: 11503
      127.42 -   134.80: 187
  Bond angle restraints: 34481
  Sorted by residual:
  angle pdb=" C   GLU A 619 "
        pdb=" N   VAL A 620 "
        pdb=" CA  VAL A 620 "
      ideal   model   delta    sigma   weight residual
     120.33  124.82   -4.49 8.00e-01 1.56e+00 3.15e+01
  angle pdb=" C   LEU A 212 "
        pdb=" N   GLU A 213 "
        pdb=" CA  GLU A 213 "
      ideal   model   delta    sigma   weight residual
     120.82  128.83   -8.01 1.50e+00 4.44e-01 2.85e+01
  angle pdb=" C   GLY A 744 "
        pdb=" N   ASP A 745 "
        pdb=" CA  ASP A 745 "
      ideal   model   delta    sigma   weight residual
     122.07  129.51   -7.44 1.43e+00 4.89e-01 2.70e+01
  angle pdb=" C   PHE B  32 "
        pdb=" CA  PHE B  32 "
        pdb=" CB  PHE B  32 "
      ideal   model   delta    sigma   weight residual
     117.23  110.87    6.36 1.36e+00 5.41e-01 2.19e+01
  angle pdb=" C   VAL A1040 "
        pdb=" N   ASP A1041 "
        pdb=" CA  ASP A1041 "
      ideal   model   delta    sigma   weight residual
     121.54  129.88   -8.34 1.91e+00 2.74e-01 1.91e+01
  ... (remaining 34476 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 14207
       17.56 -    35.12: 1236
       35.12 -    52.68: 214
       52.68 -    70.25: 56
       70.25 -    87.81: 35
  Dihedral angle restraints: 15748
    sinusoidal: 6730
      harmonic: 9018
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.12  -84.12     1      1.00e+01 1.00e-02 8.62e+01
  dihedral pdb=" CB  CYS C1082 "
           pdb=" SG  CYS C1082 "
           pdb=" SG  CYS C1126 "
           pdb=" CB  CYS C1126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -7.61  -78.39     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.42   41.58     1      1.00e+01 1.00e-02 2.42e+01
  ... (remaining 15745 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 3405
       0.073 -    0.146: 620
       0.146 -    0.218: 32
       0.218 -    0.291: 6
       0.291 -    0.364: 1
  Chirality restraints: 4064
  Sorted by residual:
  chirality pdb=" C2  NAG C1310 "
            pdb=" C1  NAG C1310 "
            pdb=" C3  NAG C1310 "
            pdb=" N2  NAG C1310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.13   -0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CB  ILE A  22 "
            pdb=" CA  ILE A  22 "
            pdb=" CG1 ILE A  22 "
            pdb=" CG2 ILE A  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CG  LEU C 390 "
            pdb=" CB  LEU C 390 "
            pdb=" CD1 LEU C 390 "
            pdb=" CD2 LEU C 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 4061 not shown)

  Planarity restraints: 4432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 208 "   -0.054 5.00e-02 4.00e+02   8.36e-02 1.12e+01
        pdb=" N   PRO A 209 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 209 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 209 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 343 "   -0.025 2.00e-02 2.50e+03   2.31e-02 6.68e+00
        pdb=" CG  ASN A 343 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 343 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 343 "    0.029 2.00e-02 2.50e+03
        pdb=" C1  NAG A1303 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 745 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.52e+00
        pdb=" CG  ASP B 745 "    0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 745 "   -0.016 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 745 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 4429 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 6915
        2.82 -     3.34: 19691
        3.34 -     3.86: 39901
        3.86 -     4.38: 45258
        4.38 -     4.90: 81552
  Nonbonded interactions: 193317
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 880 "
            pdb=" OG  SER B 884 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OH  TYR A  37 "
            pdb=" O   LEU A  54 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ALA C 879 "
            pdb=" OG1 THR C 883 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   ALA A 879 "
            pdb=" OG1 THR A 883 "
     model   vdw
     2.314 3.040
  ... (remaining 193312 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 24 through 132 or resid 165 through 677 or resid 690 throu \ 
gh 1146 or resid 1301 through 1309))
  selection = chain 'B'
  selection = (chain 'C' and (resid 24 through 132 or resid 165 through 677 or resid 690 throu \ 
gh 1146 or resid 1301 through 1309))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.950
  Check model and map are aligned:         0.210
  Set scattering table:                    0.250
  Process input model:                     68.620
  Find NCS groups from input model:        1.500
  Set up NCS constraints:                  0.120
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   84.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
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      :  0.004   0.047  25350  Z= 0.278
  Angle     :  0.749  13.392  34481  Z= 0.397
  Chirality :  0.053   0.364   4064
  Planarity :  0.006   0.084   4395
  Dihedral  : 13.801  87.806   9818
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.14), residues: 3055
  helix: -0.23 (0.17), residues: 690
  sheet:  0.53 (0.19), residues: 695
  loop : -1.34 (0.14), residues: 1670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 886 
 HIS   0.004   0.001   HIS A 207 
 PHE   0.018   0.002   PHE B1121 
 TYR   0.025   0.001   TYR C 266 
 ARG   0.004   0.000   ARG A 355 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 2.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  697 MET cc_start: 0.9057 (ptm) cc_final: 0.8812 (ptm)
REVERT: A  821 LEU cc_start: 0.8236 (mt) cc_final: 0.8014 (mp)
REVERT: B  935 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7191 (tm-30)
REVERT: B 1101 HIS cc_start: 0.7435 (m90) cc_final: 0.7229 (m90)
REVERT: C  420 ASP cc_start: 0.7270 (m-30) cc_final: 0.6806 (m-30)
REVERT: C  869 MET cc_start: 0.8521 (mtt) cc_final: 0.8279 (mtt)
REVERT: C  995 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7321 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 1.1511
  time to fit residues: 333.1597
Evaluate side-chains
  185 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 2.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 260 optimal weight:    4.9990
   chunk 233 optimal weight:    5.9990
   chunk 129 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 157 optimal weight:    7.9990
   chunk 124 optimal weight:    4.9990
   chunk 241 optimal weight:    0.0170
   chunk 93 optimal weight:    3.9990
   chunk 146 optimal weight:    5.9990
   chunk 179 optimal weight:    3.9990
   chunk 279 optimal weight:    2.9990
   overall best weight:    2.8026

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 804 GLN
A 901 GLN
A 955 ASN
A 957 GLN
A 960 ASN
B 394 ASN
B 613 GLN
B1005 GLN
C 448 ASN
C 493 GLN
C1101 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  25350  Z= 0.443
  Angle     :  0.671  18.995  34481  Z= 0.344
  Chirality :  0.050   0.233   4064
  Planarity :  0.005   0.069   4395
  Dihedral  :  7.147  59.837   4282
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  7.10 %
    Favored  : 91.46 %
  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: -0.55 (0.14), residues: 3055
  helix:  0.84 (0.19), residues: 691
  sheet:  0.47 (0.19), residues: 690
  loop : -1.28 (0.14), residues: 1674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 886 
 HIS   0.008   0.002   HIS B1064 
 PHE   0.027   0.002   PHE C 377 
 TYR   0.025   0.002   TYR C1067 
 ARG   0.005   0.001   ARG A 466 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 202
  time to evaluate  : 3.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6784 (ttm170)
REVERT: A  239 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6312 (mp10)
REVERT: A  697 MET cc_start: 0.9126 (ptm) cc_final: 0.8844 (ptm)
REVERT: A  994 ASP cc_start: 0.8071 (t70) cc_final: 0.7821 (t70)
REVERT: B  375 PHE cc_start: 0.7516 (t80) cc_final: 0.7253 (m-80)
REVERT: B  420 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8281 (p0)
REVERT: B  556 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7461 (p0)
REVERT: B  935 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7484 (tm-30)
REVERT: C  467 ASP cc_start: 0.7586 (t0) cc_final: 0.7311 (m-30)
REVERT: C  869 MET cc_start: 0.8700 (mtt) cc_final: 0.8438 (mtm)
  outliers start: 39
  outliers final: 18
  residues processed: 225
  average time/residue: 1.2415
  time to fit residues: 329.9593
Evaluate side-chains
  202 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 2.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  558 LYS
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  556 ASN
Chi-restraints excluded: chain B residue  560 LEU
Chi-restraints excluded: chain B residue  859 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  553 THR
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  875 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 155 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 232 optimal weight:    0.4980
   chunk 190 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 280 optimal weight:    0.7980
   chunk 302 optimal weight:    2.9990
   chunk 249 optimal weight:    0.3980
   chunk 277 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 224 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
A  66 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
A 613 GLN
A 935 GLN
A 965 GLN
A1005 GLN
B  52 GLN
B 218 GLN
B 394 ASN
B 804 GLN
B1005 GLN
C 334 ASN
C 448 ASN
C 493 GLN
C1101 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  25350  Z= 0.155
  Angle     :  0.511  18.126  34481  Z= 0.262
  Chirality :  0.044   0.261   4064
  Planarity :  0.004   0.053   4395
  Dihedral  :  6.545  59.826   4282
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.29 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.15), residues: 3055
  helix:  1.64 (0.20), residues: 696
  sheet:  0.58 (0.19), residues: 687
  loop : -1.12 (0.14), residues: 1672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.002   0.000   HIS C1048 
 PHE   0.024   0.001   PHE C 168 
 TYR   0.015   0.001   TYR A1067 
 ARG   0.004   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 202
  time to evaluate  : 2.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6185 (mp10)
REVERT: A  466 ARG cc_start: 0.7298 (ttp-110) cc_final: 0.6842 (ttp-110)
REVERT: A  467 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.5879 (m-30)
REVERT: A  697 MET cc_start: 0.9129 (ptm) cc_final: 0.8825 (ptm)
REVERT: A  808 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.6951 (m-30)
REVERT: B  375 PHE cc_start: 0.7433 (t80) cc_final: 0.7085 (m-80)
REVERT: B  493 GLN cc_start: 0.7754 (mt0) cc_final: 0.7469 (mt0)
REVERT: B  556 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7405 (p0)
REVERT: B  935 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: C  319 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7361 (ttt180)
REVERT: C  531 THR cc_start: 0.8153 (m) cc_final: 0.7849 (p)
REVERT: C  661 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7275 (mt-10)
REVERT: C  869 MET cc_start: 0.8606 (mtt) cc_final: 0.8400 (mtt)
  outliers start: 33
  outliers final: 15
  residues processed: 222
  average time/residue: 1.1492
  time to fit residues: 304.6497
Evaluate side-chains
  202 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 2.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  957 GLN
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  450 ASN
Chi-restraints excluded: chain B residue  556 ASN
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue 1114 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 276 optimal weight:    1.9990
   chunk 210 optimal weight:    6.9990
   chunk 145 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 133 optimal weight:    4.9990
   chunk 188 optimal weight:    4.9990
   chunk 281 optimal weight:    0.9980
   chunk 297 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 266 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 HIS
A 957 GLN
A 960 ASN
B  52 GLN
B 394 ASN
B1005 GLN
C1101 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  25350  Z= 0.232
  Angle     :  0.546  18.003  34481  Z= 0.278
  Chirality :  0.045   0.266   4064
  Planarity :  0.004   0.042   4395
  Dihedral  :  6.517  59.896   4282
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.70 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.15), residues: 3055
  helix:  1.80 (0.20), residues: 696
  sheet:  0.58 (0.19), residues: 687
  loop : -1.10 (0.14), residues: 1672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.001   HIS A1064 
 PHE   0.018   0.001   PHE C 377 
 TYR   0.019   0.001   TYR C1067 
 ARG   0.002   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 183
  time to evaluate  : 2.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6868 (mp0)
REVERT: A  239 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6323 (mp10)
REVERT: A  355 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7078 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5882 (m-30)
REVERT: A  661 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6987 (mp0)
REVERT: A  697 MET cc_start: 0.9118 (ptm) cc_final: 0.8785 (ptm)
REVERT: A  808 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.6897 (m-30)
REVERT: A  821 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8049 (mt)
REVERT: B  375 PHE cc_start: 0.7628 (t80) cc_final: 0.7332 (m-80)
REVERT: B  493 GLN cc_start: 0.7718 (mt0) cc_final: 0.7428 (mt0)
REVERT: B  556 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7401 (p0)
REVERT: B  935 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7338 (tm-30)
REVERT: C   53 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6716 (t0)
REVERT: C  319 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7326 (ttt180)
REVERT: C  326 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7329 (mp)
REVERT: C  531 THR cc_start: 0.8169 (m) cc_final: 0.7935 (p)
REVERT: C  571 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7150 (t70)
REVERT: C  661 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7284 (mt-10)
REVERT: C  869 MET cc_start: 0.8635 (mtt) cc_final: 0.8401 (mtt)
  outliers start: 47
  outliers final: 22
  residues processed: 213
  average time/residue: 1.1437
  time to fit residues: 290.3211
Evaluate side-chains
  212 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 2.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  450 ASN
Chi-restraints excluded: chain B residue  556 ASN
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 247 optimal weight:    0.8980
   chunk 168 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 221 optimal weight:    8.9990
   chunk 122 optimal weight:    8.9990
   chunk 254 optimal weight:    2.9990
   chunk 205 optimal weight:    0.0170
   chunk 0 optimal weight:    9.9990
   chunk 152 optimal weight:    5.9990
   chunk 267 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.3822

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 935 GLN
B  52 GLN
B 394 ASN
B1005 GLN
C 334 ASN
C 448 ASN
C1101 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  25350  Z= 0.239
  Angle     :  0.543  17.177  34481  Z= 0.277
  Chirality :  0.045   0.250   4064
  Planarity :  0.004   0.041   4395
  Dihedral  :  6.317  59.683   4282
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.44 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.15), residues: 3055
  helix:  1.84 (0.20), residues: 696
  sheet:  0.55 (0.19), residues: 700
  loop : -1.07 (0.15), residues: 1659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.001   HIS A1064 
 PHE   0.027   0.001   PHE C 168 
 TYR   0.018   0.001   TYR C  28 
 ARG   0.003   0.000   ARG C 457 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 185
  time to evaluate  : 2.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6855 (mp0)
REVERT: A  239 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6248 (mp10)
REVERT: A  355 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7043 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.5951 (m-30)
REVERT: A  661 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6979 (mp0)
REVERT: A  697 MET cc_start: 0.9100 (ptm) cc_final: 0.8850 (ptm)
REVERT: A  808 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7169 (m-30)
REVERT: B  335 LEU cc_start: 0.8545 (mm) cc_final: 0.8326 (mt)
REVERT: B  375 PHE cc_start: 0.7629 (t80) cc_final: 0.7319 (m-80)
REVERT: B  493 GLN cc_start: 0.7714 (mt0) cc_final: 0.7391 (mt0)
REVERT: B  556 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7380 (p0)
REVERT: B  697 MET cc_start: 0.8994 (ptm) cc_final: 0.8725 (ptp)
REVERT: C   53 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6735 (t0)
REVERT: C  319 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7406 (ttt180)
REVERT: C  326 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7373 (mp)
REVERT: C  498 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7901 (mtp85)
REVERT: C  571 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7175 (t70)
REVERT: C  661 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7290 (mt-10)
REVERT: C  869 MET cc_start: 0.8630 (mtt) cc_final: 0.8414 (mtt)
REVERT: C 1127 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7369 (m-30)
  outliers start: 51
  outliers final: 29
  residues processed: 214
  average time/residue: 1.1008
  time to fit residues: 282.0321
Evaluate side-chains
  214 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 172
  time to evaluate  : 2.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  556 ASN
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  859 THR
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  498 ARG
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  553 THR
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Chi-restraints excluded: chain C residue 1127 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 268 optimal weight:    0.0040
   chunk 58 optimal weight:    2.9990
   chunk 174 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 298 optimal weight:    1.9990
   chunk 247 optimal weight:    1.9990
   chunk 137 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 156 optimal weight:    9.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
B  52 GLN
B 394 ASN
B 437 ASN
B1005 GLN
C 405 ASN
** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1101 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  25350  Z= 0.303
  Angle     :  0.580  16.567  34481  Z= 0.296
  Chirality :  0.047   0.244   4064
  Planarity :  0.004   0.041   4395
  Dihedral  :  6.317  59.599   4282
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.41 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.15), residues: 3055
  helix:  1.73 (0.20), residues: 692
  sheet:  0.46 (0.19), residues: 702
  loop : -1.09 (0.14), residues: 1661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.022   0.002   PHE C 377 
 TYR   0.020   0.002   TYR C1067 
 ARG   0.005   0.000   ARG A 466 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 183
  time to evaluate  : 2.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6975 (mp0)
REVERT: A  190 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.6885 (mtt180)
REVERT: A  239 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6293 (mp10)
REVERT: A  355 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7103 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.5926 (m-30)
REVERT: A  661 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7080 (mp0)
REVERT: A  697 MET cc_start: 0.9091 (ptm) cc_final: 0.8849 (ptm)
REVERT: A  808 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7216 (m-30)
REVERT: A 1084 ASP cc_start: 0.7431 (t0) cc_final: 0.7113 (t0)
REVERT: B  335 LEU cc_start: 0.8602 (mm) cc_final: 0.8390 (mt)
REVERT: B  375 PHE cc_start: 0.7725 (t80) cc_final: 0.7367 (m-80)
REVERT: B  452 LEU cc_start: 0.8870 (mp) cc_final: 0.8636 (mt)
REVERT: B  493 GLN cc_start: 0.7490 (mt0) cc_final: 0.7169 (mt0)
REVERT: B  556 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7355 (p0)
REVERT: B  697 MET cc_start: 0.9044 (ptm) cc_final: 0.8803 (ptp)
REVERT: B  935 GLN cc_start: 0.7801 (tt0) cc_final: 0.7510 (tt0)
REVERT: C   53 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6804 (t0)
REVERT: C  319 ARG cc_start: 0.7675 (mmt180) cc_final: 0.7414 (ttt180)
REVERT: C  571 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7228 (t70)
REVERT: C  661 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7321 (mt-10)
REVERT: C  869 MET cc_start: 0.8636 (mtt) cc_final: 0.8405 (mtt)
REVERT: C 1113 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7626 (mt0)
  outliers start: 55
  outliers final: 33
  residues processed: 216
  average time/residue: 1.1572
  time to fit residues: 298.0732
Evaluate side-chains
  219 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 175
  time to evaluate  : 3.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue 1092 GLU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  450 ASN
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  556 ASN
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  791 THR
Chi-restraints excluded: chain B residue  859 THR
Chi-restraints excluded: chain B residue  874 THR
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  553 THR
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1113 GLN
Chi-restraints excluded: chain C residue 1114 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 287 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 169 optimal weight:    1.9990
   chunk 217 optimal weight:   10.0000
   chunk 168 optimal weight:    0.5980
   chunk 250 optimal weight:    4.9990
   chunk 166 optimal weight:    0.9990
   chunk 296 optimal weight:    0.7980
   chunk 185 optimal weight:    3.9990
   chunk 180 optimal weight:    1.9990
   chunk 137 optimal weight:    6.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 935 GLN
B  52 GLN
B 394 ASN
B 935 GLN
B1005 GLN
C 334 ASN
C1101 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  25350  Z= 0.225
  Angle     :  0.539  15.663  34481  Z= 0.275
  Chirality :  0.045   0.252   4064
  Planarity :  0.004   0.044   4395
  Dihedral  :  6.134  59.698   4282
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.93 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.15), residues: 3055
  helix:  1.82 (0.20), residues: 702
  sheet:  0.56 (0.19), residues: 689
  loop : -1.07 (0.14), residues: 1664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C1048 
 PHE   0.029   0.001   PHE C 168 
 TYR   0.018   0.001   TYR C  28 
 ARG   0.010   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 183
  time to evaluate  : 2.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6940 (mp0)
REVERT: A  190 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.6900 (mtt180)
REVERT: A  239 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6273 (mp10)
REVERT: A  355 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7067 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.5945 (m-30)
REVERT: A  661 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7057 (mp0)
REVERT: A  697 MET cc_start: 0.9063 (ptm) cc_final: 0.8834 (ptm)
REVERT: A  804 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7784 (mt0)
REVERT: A  808 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7196 (m-30)
REVERT: B  335 LEU cc_start: 0.8566 (mm) cc_final: 0.8346 (mt)
REVERT: B  375 PHE cc_start: 0.7686 (t80) cc_final: 0.7314 (m-80)
REVERT: B  493 GLN cc_start: 0.7450 (mt0) cc_final: 0.7155 (mt0)
REVERT: B  697 MET cc_start: 0.9034 (ptm) cc_final: 0.8804 (ptp)
REVERT: C   53 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6729 (t0)
REVERT: C  319 ARG cc_start: 0.7666 (mmt180) cc_final: 0.7386 (ttt180)
REVERT: C  571 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7153 (t70)
REVERT: C  661 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7286 (mt-10)
REVERT: C  869 MET cc_start: 0.8630 (mtt) cc_final: 0.8426 (mtt)
REVERT: C 1127 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7442 (m-30)
  outliers start: 59
  outliers final: 33
  residues processed: 220
  average time/residue: 1.1753
  time to fit residues: 309.3211
Evaluate side-chains
  219 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 176
  time to evaluate  : 2.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  791 THR
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  450 ASN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  859 THR
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  553 THR
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  791 THR
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Chi-restraints excluded: chain C residue 1127 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 183 optimal weight:    4.9990
   chunk 118 optimal weight:    6.9990
   chunk 177 optimal weight:    0.0870
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 188 optimal weight:    4.9990
   chunk 202 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 233 optimal weight:    4.9990
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
B  52 GLN
B 394 ASN
B 935 GLN
B1005 GLN
C1101 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  25350  Z= 0.178
  Angle     :  0.514  14.889  34481  Z= 0.264
  Chirality :  0.044   0.252   4064
  Planarity :  0.003   0.040   4395
  Dihedral  :  5.945  59.486   4282
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.41 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.15), residues: 3055
  helix:  2.04 (0.20), residues: 695
  sheet:  0.52 (0.19), residues: 707
  loop : -1.00 (0.15), residues: 1653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C  66 
 PHE   0.016   0.001   PHE C 377 
 TYR   0.017   0.001   TYR C  28 
 ARG   0.008   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 182
  time to evaluate  : 2.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6877 (mp0)
REVERT: A  190 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.6962 (mtt180)
REVERT: A  239 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6306 (mp10)
REVERT: A  355 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.6990 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.5933 (m-30)
REVERT: A  661 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6978 (mp0)
REVERT: A  697 MET cc_start: 0.9071 (ptm) cc_final: 0.8812 (ptm)
REVERT: A  808 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7373 (m-30)
REVERT: A  821 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8028 (mt)
REVERT: A  935 GLN cc_start: 0.6633 (tt0) cc_final: 0.6422 (mt0)
REVERT: A 1084 ASP cc_start: 0.7407 (t0) cc_final: 0.7127 (t0)
REVERT: B   32 PHE cc_start: 0.6473 (m-80) cc_final: 0.6203 (m-10)
REVERT: B  335 LEU cc_start: 0.8564 (mm) cc_final: 0.8321 (mt)
REVERT: B  375 PHE cc_start: 0.7685 (t80) cc_final: 0.7303 (m-80)
REVERT: B  493 GLN cc_start: 0.7481 (mt0) cc_final: 0.7196 (mt0)
REVERT: B  697 MET cc_start: 0.9004 (ptm) cc_final: 0.8765 (ptp)
REVERT: B  935 GLN cc_start: 0.7685 (tt0) cc_final: 0.7378 (tt0)
REVERT: C   53 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6595 (t0)
REVERT: C  319 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7374 (ttt180)
REVERT: C  571 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7144 (t70)
REVERT: C  661 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7276 (mt-10)
REVERT: C 1127 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7298 (m-30)
  outliers start: 46
  outliers final: 28
  residues processed: 213
  average time/residue: 1.0462
  time to fit residues: 268.3196
Evaluate side-chains
  213 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 174
  time to evaluate  : 2.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  791 THR
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  875 SER
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  617 CYS
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  791 THR
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Chi-restraints excluded: chain C residue 1127 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 270 optimal weight:    0.5980
   chunk 284 optimal weight:    2.9990
   chunk 259 optimal weight:    5.9990
   chunk 276 optimal weight:    2.9990
   chunk 166 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 217 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 249 optimal weight:    2.9990
   chunk 261 optimal weight:    3.9990
   chunk 275 optimal weight:    0.8980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 GLN
B 394 ASN
B1005 GLN
C1101 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  25350  Z= 0.278
  Angle     :  0.564  14.800  34481  Z= 0.289
  Chirality :  0.046   0.240   4064
  Planarity :  0.004   0.041   4395
  Dihedral  :  6.063  59.833   4282
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.30 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.15), residues: 3055
  helix:  1.86 (0.20), residues: 692
  sheet:  0.46 (0.19), residues: 701
  loop : -1.04 (0.15), residues: 1662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.028   0.001   PHE C 168 
 TYR   0.020   0.001   TYR C1067 
 ARG   0.007   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 179
  time to evaluate  : 3.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6917 (mp0)
REVERT: A  190 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.6920 (mtt180)
REVERT: A  239 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6329 (mp10)
REVERT: A  355 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7070 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.5897 (m-30)
REVERT: A  661 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7066 (mp0)
REVERT: A  697 MET cc_start: 0.9065 (ptm) cc_final: 0.8830 (ptm)
REVERT: A  808 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (m-30)
REVERT: A 1084 ASP cc_start: 0.7631 (t0) cc_final: 0.7402 (t0)
REVERT: B  335 LEU cc_start: 0.8596 (mm) cc_final: 0.8341 (mt)
REVERT: B  375 PHE cc_start: 0.7684 (t80) cc_final: 0.7294 (m-80)
REVERT: B  493 GLN cc_start: 0.7490 (mt0) cc_final: 0.7195 (mt0)
REVERT: C   53 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6782 (t0)
REVERT: C  319 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7388 (ttt180)
REVERT: C  571 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7194 (t70)
REVERT: C  661 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7292 (mt-10)
REVERT: C 1127 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7448 (m-30)
  outliers start: 51
  outliers final: 35
  residues processed: 217
  average time/residue: 1.0827
  time to fit residues: 283.6891
Evaluate side-chains
  220 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 175
  time to evaluate  : 3.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  791 THR
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  875 SER
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  874 THR
Chi-restraints excluded: chain B residue  988 GLU
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  617 CYS
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  791 THR
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Chi-restraints excluded: chain C residue 1127 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 181 optimal weight:    2.9990
   chunk 292 optimal weight:    2.9990
   chunk 178 optimal weight:    1.9990
   chunk 138 optimal weight:    8.9990
   chunk 203 optimal weight:    5.9990
   chunk 306 optimal weight:    1.9990
   chunk 282 optimal weight:    2.9990
   chunk 244 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 188 optimal weight:    3.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
A 613 GLN
B  52 GLN
B 394 ASN
B 556 ASN
B1005 GLN
** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1101 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  25350  Z= 0.412
  Angle     :  0.632  14.740  34481  Z= 0.324
  Chirality :  0.049   0.236   4064
  Planarity :  0.004   0.042   4395
  Dihedral  :  6.329  59.979   4282
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.41 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.15), residues: 3055
  helix:  1.60 (0.20), residues: 687
  sheet:  0.32 (0.19), residues: 696
  loop : -1.08 (0.15), residues: 1672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 104 
 HIS   0.006   0.001   HIS A1064 
 PHE   0.029   0.002   PHE C 377 
 TYR   0.022   0.002   TYR C1067 
 ARG   0.007   0.000   ARG C 190 

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

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

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6110 Ramachandran restraints generated.
    3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 182
  time to evaluate  : 2.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6794 (mp0)
REVERT: A  190 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7221 (mtp85)
REVERT: A  355 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7173 (ttp-170)
REVERT: A  467 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5940 (m-30)
REVERT: A  499 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8082 (Cg_exo)
REVERT: A  661 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7052 (mp0)
REVERT: A  808 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7297 (m-30)
REVERT: B  375 PHE cc_start: 0.7713 (t80) cc_final: 0.7289 (m-80)
REVERT: B  493 GLN cc_start: 0.7430 (mt0) cc_final: 0.7139 (mt0)
REVERT: C  319 ARG cc_start: 0.7657 (mmt180) cc_final: 0.7385 (ttt180)
REVERT: C  571 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7207 (t70)
REVERT: C  661 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7322 (mt-10)
  outliers start: 49
  outliers final: 37
  residues processed: 218
  average time/residue: 1.1051
  time to fit residues: 289.6339
Evaluate side-chains
  218 residues out of total 2692 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 2.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 GLN
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  467 ASP
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  661 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue  787 GLN
Chi-restraints excluded: chain A residue  791 THR
Chi-restraints excluded: chain A residue  808 ASP
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  875 SER
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  874 THR
Chi-restraints excluded: chain B residue 1094 VAL
Chi-restraints excluded: chain C residue   26 GLN
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  546 LEU
Chi-restraints excluded: chain C residue  571 ASP
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  617 CYS
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  661 GLU
Chi-restraints excluded: chain C residue  738 CYS
Chi-restraints excluded: chain C residue  791 THR
Chi-restraints excluded: chain C residue  875 SER
Chi-restraints excluded: chain C residue 1114 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 308
   random chunks:
   chunk 194 optimal weight:    0.8980
   chunk 260 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 225 optimal weight:    0.3980
   chunk 36 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 244 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 251 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
B  52 GLN
B 394 ASN
B1005 GLN
C1101 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.176566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.125195 restraints weight = 25954.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.70
r_work: 0.3049 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  25350  Z= 0.225
  Angle     :  0.550  14.017  34481  Z= 0.282
  Chirality :  0.045   0.251   4064
  Planarity :  0.004   0.040   4395
  Dihedral  :  6.103  59.581   4282
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.78 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.15), residues: 3055
  helix:  1.87 (0.20), residues: 691
  sheet:  0.38 (0.19), residues: 709
  loop : -1.02 (0.15), residues: 1655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C  66 
 PHE   0.032   0.001   PHE C 168 
 TYR   0.017   0.001   TYR C1067 
 ARG   0.007   0.000   ARG C 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6561.03 seconds
wall clock time: 116 minutes 52.09 seconds (7012.09 seconds total)