Starting phenix.real_space_refine
on Wed Feb 14 01:24:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/02_2024/6m3w_30072.pdb"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    5190      2.51       5
     N    1386      2.21       5
     O    1692      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  747": "NH1" <-> "NH2"
    Residue "A ARG  996": "NH1" <-> "NH2"
    Residue "B ARG  747": "NH1" <-> "NH2"
    Residue "B ARG  996": "NH1" <-> "NH2"
    Residue "C ARG  747": "NH1" <-> "NH2"
    Residue "C ARG  996": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 8307
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2657
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 11, 'TRANS': 332}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2657
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 11, 'TRANS': 332}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2657
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 11, 'TRANS': 332}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
    Chain: "B"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
    Chain: "C"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
  Time building chain proxies: 4.88, per 1000 atoms: 0.59
  Number of scatterers: 8307
  At special positions: 0
  Unit cell: (73, 73, 208, 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      39     16.00
     O    1692      8.00
     N    1386      7.00
     C    5190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 720 " - pdb=" SG  CYS A 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 725 " - pdb=" SG  CYS A 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1014 " - pdb=" SG  CYS A1025 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1064 " - pdb=" SG  CYS A1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 720 " - pdb=" SG  CYS B 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 725 " - pdb=" SG  CYS B 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1014 " - pdb=" SG  CYS B1025 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1064 " - pdb=" SG  CYS B1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 720 " - pdb=" SG  CYS C 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 725 " - pdb=" SG  CYS C 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1014 " - pdb=" SG  CYS C1025 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1064 " - pdb=" SG  CYS C1108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1201 " - " ASN A1176 "
      " NAG A1202 " - " ASN A1155 "
      " NAG A1203 " - " ASN A1140 "
      " NAG A1204 " - " ASN A1116 "
      " NAG A1205 " - " ASN A1080 "
      " NAG A1206 " - " ASN A1056 "
      " NAG A1207 " - " ASN A 699 "
      " NAG A1208 " - " ASN A 691 "
      " NAG B1201 " - " ASN B1176 "
      " NAG B1202 " - " ASN B1155 "
      " NAG B1203 " - " ASN B1140 "
      " NAG B1204 " - " ASN B1116 "
      " NAG B1205 " - " ASN B1080 "
      " NAG B1206 " - " ASN B1056 "
      " NAG B1207 " - " ASN B 699 "
      " NAG B1208 " - " ASN B 691 "
      " NAG C1201 " - " ASN C1176 "
      " NAG C1202 " - " ASN C1155 "
      " NAG C1203 " - " ASN C1140 "
      " NAG C1204 " - " ASN C1116 "
      " NAG C1205 " - " ASN C1080 "
      " NAG C1206 " - " ASN C1056 "
      " NAG C1207 " - " ASN C 699 "
      " NAG C1208 " - " ASN C 691 "
  Time building additional restraints: 3.49
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1962

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 12 sheets defined
      50.6% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 728 through 736
      removed outlier: 3.781A  pdb=" N   ALA A 732 " --> pdb=" O   SER A 728 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 753
      removed outlier: 3.559A  pdb=" N   GLN A 744 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 1014
      removed outlier: 3.629A  pdb=" N   ALA A 906 " --> pdb=" O   GLN A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1137
      removed outlier: 3.779A  pdb=" N   TYR A1137 " --> pdb=" O   GLU A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1154
      removed outlier: 3.588A  pdb=" N   ILE A1154 " --> pdb=" O   ASP A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1178
      removed outlier: 3.525A  pdb=" N   SER A1178 " --> pdb=" O   ASN A1174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 724
    Processing helix  chain 'B' and resid 728 through 736
      removed outlier: 3.781A  pdb=" N   ALA B 732 " --> pdb=" O   SER B 728 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU B 736 " --> pdb=" O   ALA B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 753
      removed outlier: 3.558A  pdb=" N   GLN B 744 " --> pdb=" O   SER B 740 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 902 through 1014
      removed outlier: 3.629A  pdb=" N   ALA B 906 " --> pdb=" O   GLN B 902 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1137
      removed outlier: 3.779A  pdb=" N   TYR B1137 " --> pdb=" O   GLU B1133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1149 through 1154
      removed outlier: 3.588A  pdb=" N   ILE B1154 " --> pdb=" O   ASP B1150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1162 through 1178
      removed outlier: 3.526A  pdb=" N   SER B1178 " --> pdb=" O   ASN B1174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 719 through 724
    Processing helix  chain 'C' and resid 728 through 736
      removed outlier: 3.782A  pdb=" N   ALA C 732 " --> pdb=" O   SER C 728 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU C 736 " --> pdb=" O   ALA C 732 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 740 through 753
      removed outlier: 3.559A  pdb=" N   GLN C 744 " --> pdb=" O   SER C 740 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA C 753 " --> pdb=" O   LEU C 749 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 902 through 1014
      removed outlier: 3.630A  pdb=" N   ALA C 906 " --> pdb=" O   GLN C 902 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1129 through 1137
      removed outlier: 3.779A  pdb=" N   TYR C1137 " --> pdb=" O   GLU C1133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1149 through 1154
      removed outlier: 3.589A  pdb=" N   ILE C1154 " --> pdb=" O   ASP C1150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1162 through 1178
      removed outlier: 3.526A  pdb=" N   SER C1178 " --> pdb=" O   ASN C1174 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG A1055 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN A1053 " --> pdb=" O   THR A 698 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE A 700 " --> pdb=" O   PRO A1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE A 702 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR A1049 " --> pdb=" O   ILE A 702 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE A 704 " --> pdb=" O   VAL A1047 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL A1047 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 709 " --> pdb=" O   VAL A1042 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG A1055 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN A1053 " --> pdb=" O   THR A 698 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE A 700 " --> pdb=" O   PRO A1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE A 702 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR A1049 " --> pdb=" O   ILE A 702 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE A 704 " --> pdb=" O   VAL A1047 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL A1047 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   TYR A1049 " --> pdb=" O   HIS A1030 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   HIS A1030 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1071 through 1072
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1077 through 1078
    Processing sheet with id=AA5, first strand: chain 'B' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG B1055 " --> pdb=" O   ILE B 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN B1053 " --> pdb=" O   THR B 698 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE B 700 " --> pdb=" O   PRO B1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE B 702 " --> pdb=" O   TYR B1049 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR B1049 " --> pdb=" O   ILE B 702 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE B 704 " --> pdb=" O   VAL B1047 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B1047 " --> pdb=" O   ILE B 704 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET B 709 " --> pdb=" O   VAL B1042 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG B1055 " --> pdb=" O   ILE B 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN B1053 " --> pdb=" O   THR B 698 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE B 700 " --> pdb=" O   PRO B1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE B 702 " --> pdb=" O   TYR B1049 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR B1049 " --> pdb=" O   ILE B 702 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE B 704 " --> pdb=" O   VAL B1047 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B1047 " --> pdb=" O   ILE B 704 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   TYR B1049 " --> pdb=" O   HIS B1030 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   HIS B1030 " --> pdb=" O   TYR B1049 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1071 through 1072
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1077 through 1078
    Processing sheet with id=AA9, first strand: chain 'C' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG C1055 " --> pdb=" O   ILE C 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN C1053 " --> pdb=" O   THR C 698 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   PHE C 700 " --> pdb=" O   PRO C1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE C 702 " --> pdb=" O   TYR C1049 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   TYR C1049 " --> pdb=" O   ILE C 702 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE C 704 " --> pdb=" O   VAL C1047 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL C1047 " --> pdb=" O   ILE C 704 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET C 709 " --> pdb=" O   VAL C1042 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 692 through 704
      removed outlier: 3.575A  pdb=" N   ARG C1055 " --> pdb=" O   ILE C 696 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN C1053 " --> pdb=" O   THR C 698 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   PHE C 700 " --> pdb=" O   PRO C1051 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE C 702 " --> pdb=" O   TYR C1049 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   TYR C1049 " --> pdb=" O   ILE C 702 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE C 704 " --> pdb=" O   VAL C1047 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL C1047 " --> pdb=" O   ILE C 704 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   TYR C1049 " --> pdb=" O   HIS C1030 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   HIS C1030 " --> pdb=" O   TYR C1049 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 1071 through 1072
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1077 through 1078

    489 hydrogen bonds defined for protein.
    1422 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: 2.38

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2584
        1.34 -     1.46: 1565
        1.46 -     1.57: 4227
        1.57 -     1.69: 3
        1.69 -     1.81: 54
  Bond restraints: 8433
  Sorted by residual:
  bond pdb=" C1  NAG C1205 "
       pdb=" O5  NAG C1205 "
    ideal  model  delta    sigma   weight residual
    1.406  1.518 -0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" C1  NAG A1202 "
       pdb=" O5  NAG A1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.516 -0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" C1  NAG B1202 "
       pdb=" O5  NAG B1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.515 -0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C1  NAG B1205 "
       pdb=" O5  NAG B1205 "
    ideal  model  delta    sigma   weight residual
    1.406  1.512 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C1  NAG A1205 "
       pdb=" O5  NAG A1205 "
    ideal  model  delta    sigma   weight residual
    1.406  1.512 -0.106 2.00e-02 2.50e+03 2.79e+01
  ... (remaining 8428 not shown)

  Histogram of bond angle deviations from ideal:
       98.87 -   105.91: 165
      105.91 -   112.96: 4760
      112.96 -   120.00: 2915
      120.00 -   127.04: 3556
      127.04 -   134.08: 52
  Bond angle restraints: 11448
  Sorted by residual:
  angle pdb=" N   LEU C1148 "
        pdb=" CA  LEU C1148 "
        pdb=" C   LEU C1148 "
      ideal   model   delta    sigma   weight residual
     111.02  116.69   -5.67 1.22e+00 6.72e-01 2.16e+01
  angle pdb=" N   LEU B1148 "
        pdb=" CA  LEU B1148 "
        pdb=" C   LEU B1148 "
      ideal   model   delta    sigma   weight residual
     111.02  116.69   -5.67 1.22e+00 6.72e-01 2.16e+01
  angle pdb=" N   LEU A1148 "
        pdb=" CA  LEU A1148 "
        pdb=" C   LEU A1148 "
      ideal   model   delta    sigma   weight residual
     111.02  116.66   -5.64 1.22e+00 6.72e-01 2.14e+01
  angle pdb=" C   ASP A1147 "
        pdb=" N   LEU A1148 "
        pdb=" CA  LEU A1148 "
      ideal   model   delta    sigma   weight residual
     120.79  125.79   -5.00 1.39e+00 5.18e-01 1.30e+01
  angle pdb=" C   ASP B1147 "
        pdb=" N   LEU B1148 "
        pdb=" CA  LEU B1148 "
      ideal   model   delta    sigma   weight residual
     120.79  125.79   -5.00 1.39e+00 5.18e-01 1.29e+01
  ... (remaining 11443 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.13: 5035
       22.13 -    44.27: 255
       44.27 -    66.40: 44
       66.40 -    88.54: 67
       88.54 -   110.67: 44
  Dihedral angle restraints: 5445
    sinusoidal: 2430
      harmonic: 3015
  Sorted by residual:
  dihedral pdb=" CA  GLN A1124 "
           pdb=" C   GLN A1124 "
           pdb=" N   PRO A1125 "
           pdb=" CA  PRO A1125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -134.26  -45.74     0      5.00e+00 4.00e-02 8.37e+01
  dihedral pdb=" CA  GLN B1124 "
           pdb=" C   GLN B1124 "
           pdb=" N   PRO B1125 "
           pdb=" CA  PRO B1125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.26  -45.74     0      5.00e+00 4.00e-02 8.37e+01
  dihedral pdb=" CA  GLN C1124 "
           pdb=" C   GLN C1124 "
           pdb=" N   PRO C1125 "
           pdb=" CA  PRO C1125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.31  -45.69     0      5.00e+00 4.00e-02 8.35e+01
  ... (remaining 5442 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1261
       0.110 -    0.220: 140
       0.220 -    0.331: 12
       0.331 -    0.441: 1
       0.441 -    0.551: 5
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" C1  NAG A1207 "
            pdb=" ND2 ASN A 699 "
            pdb=" C2  NAG A1207 "
            pdb=" O5  NAG A1207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.85   -0.55 2.00e-01 2.50e+01 7.59e+00
  chirality pdb=" C1  NAG C1207 "
            pdb=" ND2 ASN C 699 "
            pdb=" C2  NAG C1207 "
            pdb=" O5  NAG C1207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.86   -0.54 2.00e-01 2.50e+01 7.34e+00
  chirality pdb=" C1  NAG B1207 "
            pdb=" ND2 ASN B 699 "
            pdb=" C2  NAG B1207 "
            pdb=" O5  NAG B1207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.89   -0.51 2.00e-01 2.50e+01 6.57e+00
  ... (remaining 1416 not shown)

  Planarity restraints: 1485
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C1143 "    0.048 5.00e-02 4.00e+02   7.32e-02 8.56e+00
        pdb=" N   PRO C1144 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO C1144 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C1144 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B1143 "    0.048 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO B1144 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B1144 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B1144 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1143 "   -0.048 5.00e-02 4.00e+02   7.28e-02 8.48e+00
        pdb=" N   PRO A1144 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A1144 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A1144 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1482 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2120
        2.79 -     3.32: 8589
        3.32 -     3.85: 14709
        3.85 -     4.37: 16295
        4.37 -     4.90: 26427
  Nonbonded interactions: 68140
  Sorted by model distance:
  nonbonded pdb=" O   GLY B1149 "
            pdb=" OG  SER B1152 "
     model   vdw
     2.264 2.440
  nonbonded pdb=" O   GLY C1149 "
            pdb=" OG  SER C1152 "
     model   vdw
     2.264 2.440
  nonbonded pdb=" O   GLY A1149 "
            pdb=" OG  SER A1152 "
     model   vdw
     2.264 2.440
  nonbonded pdb=" OD2 ASP A1145 "
            pdb=" OG  SER C 956 "
     model   vdw
     2.286 2.440
  nonbonded pdb=" O   GLU B 918 "
            pdb=" OG1 THR B 922 "
     model   vdw
     2.293 2.440
  ... (remaining 68135 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  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:          10.350
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.640
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
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      :  0.011   0.112   8433  Z= 0.726
  Angle     :  1.307  10.499  11448  Z= 0.688
  Chirality :  0.078   0.551   1419
  Planarity :  0.009   0.073   1461
  Dihedral  : 20.556 110.670   3447
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  2.99 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.60 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.25 (0.20), residues: 1020
  helix: -1.53 (0.18), residues: 498
  sheet: -3.57 (0.43), residues: 99
  loop : -4.27 (0.21), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.006   TRP B1084 
 HIS   0.006   0.002   HIS B1030 
 PHE   0.038   0.006   PHE C 952 
 TYR   0.023   0.004   TYR B1029 
 ARG   0.011   0.002   ARG B1055 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 227
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  907 ASN cc_start: 0.7897 (m-40) cc_final: 0.7552 (p0)
REVERT: A  989 TYR cc_start: 0.8308 (t80) cc_final: 0.7816 (t80)
REVERT: A 1070 TYR cc_start: 0.7321 (m-80) cc_final: 0.6850 (m-80)
REVERT: B  907 ASN cc_start: 0.7892 (m-40) cc_final: 0.7572 (p0)
REVERT: B  989 TYR cc_start: 0.8291 (t80) cc_final: 0.7921 (t80)
REVERT: C  907 ASN cc_start: 0.7800 (m-40) cc_final: 0.7354 (p0)
REVERT: C  976 ASP cc_start: 0.7541 (m-30) cc_final: 0.6704 (m-30)
REVERT: C  994 LEU cc_start: 0.9439 (mt) cc_final: 0.9213 (tp)
REVERT: C 1130 PHE cc_start: 0.8655 (m-80) cc_final: 0.8452 (m-80)
  outliers start: 6
  outliers final: 0
  residues processed: 233
  average time/residue: 0.2534
  time to fit residues: 77.0462
Evaluate side-chains
  126 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1036 GLN
A1090 ASN
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1036 GLN
B1065 HIS
C 744 GLN
C 993 GLN
C1090 ASN
C1141 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8433  Z= 0.247
  Angle     :  0.856   9.103  11448  Z= 0.408
  Chirality :  0.059   0.404   1419
  Planarity :  0.005   0.057   1461
  Dihedral  : 18.333  95.317   1590
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 11.41 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.24), residues: 1020
  helix:  0.09 (0.21), residues: 492
  sheet: -3.16 (0.44), residues: 117
  loop : -3.66 (0.24), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1084 
 HIS   0.003   0.001   HIS C1030 
 PHE   0.021   0.002   PHE B1079 
 TYR   0.012   0.001   TYR C 989 
 ARG   0.004   0.001   ARG C1073 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  976 ASP cc_start: 0.7253 (m-30) cc_final: 0.6748 (m-30)
REVERT: B  976 ASP cc_start: 0.7739 (m-30) cc_final: 0.6772 (m-30)
REVERT: B 1131 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7989 (mmtm)
REVERT: B 1166 ASP cc_start: 0.8045 (m-30) cc_final: 0.7671 (t0)
REVERT: C  976 ASP cc_start: 0.7357 (m-30) cc_final: 0.6986 (m-30)
REVERT: C  977 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7933 (mpt-90)
REVERT: C 1065 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8306 (t-90)
REVERT: C 1166 ASP cc_start: 0.8068 (m-30) cc_final: 0.7781 (t0)
  outliers start: 34
  outliers final: 15
  residues processed: 180
  average time/residue: 0.2378
  time to fit residues: 56.9097
Evaluate side-chains
  135 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1176 ASN
Chi-restraints excluded: chain B residue  972 GLU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue  990 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  972 GLU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1065 HIS
Chi-restraints excluded: chain C residue 1076 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 74 optimal weight:    0.2980
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1141 HIS
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8433  Z= 0.304
  Angle     :  0.838   9.724  11448  Z= 0.399
  Chirality :  0.057   0.372   1419
  Planarity :  0.005   0.048   1461
  Dihedral  : 15.183  90.048   1590
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 14.29 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.24), residues: 1020
  helix:  0.51 (0.21), residues: 495
  sheet: -3.15 (0.43), residues: 117
  loop : -3.68 (0.24), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C1084 
 HIS   0.009   0.001   HIS B1065 
 PHE   0.017   0.002   PHE B1057 
 TYR   0.011   0.001   TYR C1029 
 ARG   0.005   0.001   ARG A 977 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1130 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (t80)
REVERT: B  996 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7252 (tpp-160)
REVERT: B 1131 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7931 (mmtm)
REVERT: B 1166 ASP cc_start: 0.7983 (m-30) cc_final: 0.7594 (t0)
REVERT: C 1065 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8393 (t-90)
REVERT: C 1166 ASP cc_start: 0.8064 (m-30) cc_final: 0.7780 (t0)
  outliers start: 40
  outliers final: 24
  residues processed: 147
  average time/residue: 0.2265
  time to fit residues: 44.2452
Evaluate side-chains
  127 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1130 PHE
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue  990 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain B residue 1130 PHE
Chi-restraints excluded: chain B residue 1176 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  978 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1065 HIS
Chi-restraints excluded: chain C residue 1130 PHE
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1090 ASN
A1141 HIS
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8433  Z= 0.244
  Angle     :  0.769   8.841  11448  Z= 0.366
  Chirality :  0.055   0.370   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 13.499  85.082   1590
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 14.73 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.25), residues: 1020
  helix:  0.93 (0.22), residues: 495
  sheet: -2.74 (0.38), residues: 141
  loop : -3.66 (0.26), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1084 
 HIS   0.002   0.001   HIS B1030 
 PHE   0.013   0.002   PHE B1057 
 TYR   0.010   0.001   TYR C 738 
 ARG   0.004   0.001   ARG C1073 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1065 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7786 (m-70)
REVERT: B  976 ASP cc_start: 0.7656 (m-30) cc_final: 0.6807 (m-30)
REVERT: B  977 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7621 (mmt90)
REVERT: B 1020 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8543 (mtpp)
REVERT: B 1166 ASP cc_start: 0.7994 (m-30) cc_final: 0.7685 (t0)
REVERT: C  977 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (mmt90)
REVERT: C 1130 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8170 (t80)
REVERT: C 1166 ASP cc_start: 0.7989 (m-30) cc_final: 0.7744 (t0)
  outliers start: 43
  outliers final: 22
  residues processed: 151
  average time/residue: 0.2307
  time to fit residues: 46.0521
Evaluate side-chains
  131 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1130 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    0.4980
   chunk 40 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0570
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.0300

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8433  Z= 0.247
  Angle     :  0.745   8.773  11448  Z= 0.358
  Chirality :  0.053   0.356   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 12.701  80.747   1590
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.83 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.25), residues: 1020
  helix:  1.06 (0.22), residues: 495
  sheet: -2.79 (0.39), residues: 132
  loop : -3.73 (0.24), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1084 
 HIS   0.003   0.001   HIS A1030 
 PHE   0.013   0.002   PHE B1057 
 TYR   0.009   0.001   TYR C 738 
 ARG   0.004   0.001   ARG C 965 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1065 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7741 (m-70)
REVERT: B  977 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7573 (mmt90)
REVERT: B 1166 ASP cc_start: 0.8010 (m-30) cc_final: 0.7733 (t0)
REVERT: C 1011 MET cc_start: 0.8278 (ppp) cc_final: 0.7792 (ppp)
REVERT: C 1130 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8377 (t80)
REVERT: C 1166 ASP cc_start: 0.8012 (m-30) cc_final: 0.7762 (t0)
  outliers start: 36
  outliers final: 29
  residues processed: 129
  average time/residue: 0.2227
  time to fit residues: 38.9770
Evaluate side-chains
  129 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1176 ASN
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1071 PHE
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1130 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 32 optimal weight:    0.1980
   chunk 51 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 744 GLN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 984 GLN
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8433  Z= 0.232
  Angle     :  0.721   8.666  11448  Z= 0.347
  Chirality :  0.052   0.347   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 11.927  76.145   1590
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 17.61 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.25), residues: 1020
  helix:  1.17 (0.21), residues: 498
  sheet: -3.21 (0.35), residues: 162
  loop : -3.96 (0.23), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B1084 
 HIS   0.003   0.001   HIS B1030 
 PHE   0.013   0.002   PHE C1057 
 TYR   0.008   0.001   TYR A 989 
 ARG   0.004   0.001   ARG B1073 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 110
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  744 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.5941 (tt0)
REVERT: A 1065 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7678 (m-70)
REVERT: B  977 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7578 (mmt90)
REVERT: B 1011 MET cc_start: 0.7991 (ppp) cc_final: 0.7469 (ppp)
REVERT: B 1166 ASP cc_start: 0.8029 (m-30) cc_final: 0.7808 (t0)
REVERT: C  977 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7457 (mmt90)
REVERT: C  982 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7635 (mtp180)
REVERT: C 1011 MET cc_start: 0.8388 (ppp) cc_final: 0.7900 (ppp)
REVERT: C 1130 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8550 (t80)
REVERT: C 1166 ASP cc_start: 0.7958 (m-30) cc_final: 0.7744 (t0)
  outliers start: 46
  outliers final: 32
  residues processed: 141
  average time/residue: 0.2015
  time to fit residues: 39.1385
Evaluate side-chains
  130 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  744 GLN
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  692 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1071 PHE
Chi-restraints excluded: chain C residue 1073 ARG
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1130 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.5001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8433  Z= 0.252
  Angle     :  0.730   9.755  11448  Z= 0.356
  Chirality :  0.052   0.324   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 11.488  72.790   1590
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 19.16 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.24), residues: 1020
  helix:  1.10 (0.21), residues: 498
  sheet: -2.75 (0.39), residues: 132
  loop : -3.81 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1084 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.013   0.002   PHE C1057 
 TYR   0.009   0.001   TYR B1120 
 ARG   0.003   0.001   ARG C 965 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  936 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: A 1065 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7777 (m-70)
REVERT: B  977 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7422 (mmt90)
REVERT: B 1011 MET cc_start: 0.8032 (ppp) cc_final: 0.7526 (ppp)
REVERT: B 1020 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8296 (mtpp)
REVERT: C  977 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7484 (mmt90)
REVERT: C 1011 MET cc_start: 0.8392 (ppp) cc_final: 0.7909 (ppp)
REVERT: C 1130 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8530 (t80)
REVERT: C 1166 ASP cc_start: 0.7973 (m-30) cc_final: 0.7748 (t0)
  outliers start: 47
  outliers final: 36
  residues processed: 133
  average time/residue: 0.2426
  time to fit residues: 42.8215
Evaluate side-chains
  132 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  692 ASN
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  692 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1045 LEU
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1084 TRP
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1071 PHE
Chi-restraints excluded: chain C residue 1073 ARG
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1130 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0470
   chunk 66 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0170
   chunk 85 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9318

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.5193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8433  Z= 0.233
  Angle     :  0.714  12.202  11448  Z= 0.347
  Chirality :  0.051   0.313   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 11.051  69.643   1590
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 20.04 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.24), residues: 1020
  helix:  1.13 (0.22), residues: 498
  sheet: -2.64 (0.40), residues: 132
  loop : -3.80 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B1084 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.012   0.002   PHE C1057 
 TYR   0.008   0.001   TYR A1049 
 ARG   0.003   0.001   ARG B 965 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1065 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7769 (m-70)
REVERT: B  977 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7360 (mmt90)
REVERT: B  982 ARG cc_start: 0.8814 (mtp85) cc_final: 0.7955 (mtp85)
REVERT: B 1011 MET cc_start: 0.8093 (ppp) cc_final: 0.7615 (ppp)
REVERT: B 1014 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7004 (m)
REVERT: B 1020 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8264 (mtpp)
REVERT: C  977 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7511 (mmt90)
REVERT: C 1011 MET cc_start: 0.8396 (ppp) cc_final: 0.7914 (ppp)
  outliers start: 50
  outliers final: 37
  residues processed: 138
  average time/residue: 0.2158
  time to fit residues: 40.2013
Evaluate side-chains
  136 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 95
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  692 ASN
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1176 ASN
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  692 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue 1014 CYS
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1045 LEU
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1112 ILE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 993 GLN
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8433  Z= 0.244
  Angle     :  0.724  14.194  11448  Z= 0.353
  Chirality :  0.051   0.304   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 10.650  66.206   1590
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 21.04 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.24), residues: 1020
  helix:  1.05 (0.21), residues: 498
  sheet: -2.52 (0.41), residues: 132
  loop : -3.77 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1084 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.012   0.002   PHE C1057 
 TYR   0.009   0.001   TYR B 989 
 ARG   0.003   0.001   ARG C 965 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  936 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: A  982 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.7850 (mtp85)
REVERT: A  984 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8224 (mt0)
REVERT: A 1065 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7746 (m-70)
REVERT: B  982 ARG cc_start: 0.8790 (mtp85) cc_final: 0.7932 (mtp85)
REVERT: B 1011 MET cc_start: 0.8117 (ppp) cc_final: 0.7637 (ppp)
REVERT: B 1014 CYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7046 (m)
REVERT: C  977 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7757 (mmt90)
REVERT: C 1011 MET cc_start: 0.8403 (ppp) cc_final: 0.7972 (ppp)
REVERT: C 1073 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7331 (ptm160)
  outliers start: 46
  outliers final: 34
  residues processed: 131
  average time/residue: 0.2310
  time to fit residues: 40.4275
Evaluate side-chains
  132 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  692 ASN
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  984 GLN
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  692 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  978 LEU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue  990 VAL
Chi-restraints excluded: chain B residue 1014 CYS
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1112 ILE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  949 SER
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1073 ARG
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 993 GLN
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8433  Z= 0.286
  Angle     :  0.752  13.966  11448  Z= 0.370
  Chirality :  0.051   0.292   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 10.395  62.807   1590
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 21.93 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.24), residues: 1020
  helix:  0.98 (0.21), residues: 498
  sheet: -2.45 (0.41), residues: 132
  loop : -3.79 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP C1084 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.013   0.002   PHE B1057 
 TYR   0.009   0.001   TYR B1120 
 ARG   0.005   0.001   ARG A 982 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  936 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: A 1065 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7883 (m-70)
REVERT: B  977 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7482 (mmt90)
REVERT: B 1011 MET cc_start: 0.8162 (ppp) cc_final: 0.7659 (ppp)
REVERT: B 1014 CYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7111 (m)
REVERT: C  977 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7724 (mmt90)
REVERT: C 1011 MET cc_start: 0.8435 (ppp) cc_final: 0.7965 (ppp)
  outliers start: 41
  outliers final: 32
  residues processed: 124
  average time/residue: 0.2223
  time to fit residues: 37.4267
Evaluate side-chains
  130 residues out of total 903 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  692 ASN
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  691 ASN
Chi-restraints excluded: chain B residue  692 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  988 THR
Chi-restraints excluded: chain B residue  990 VAL
Chi-restraints excluded: chain B residue 1014 CYS
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1112 ILE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  691 ASN
Chi-restraints excluded: chain C residue  977 ARG
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue  994 LEU
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1045 LEU
Chi-restraints excluded: chain C residue 1073 ARG
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1168 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.071412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.061707 restraints weight = 38003.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.063240 restraints weight = 23899.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.064335 restraints weight = 17023.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8433  Z= 0.247
  Angle     :  0.733  14.385  11448  Z= 0.360
  Chirality :  0.050   0.297   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 10.127  60.297   1590
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.48 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.25), residues: 1020
  helix:  1.06 (0.21), residues: 498
  sheet: -2.71 (0.38), residues: 162
  loop : -3.87 (0.24), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1084 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.013   0.002   PHE C1092 
 TYR   0.011   0.001   TYR C1029 
 ARG   0.005   0.001   ARG B 747 

===============================================================================
Job complete
usr+sys time: 1877.35 seconds
wall clock time: 35 minutes 4.31 seconds (2104.31 seconds total)