Starting phenix.real_space_refine
on Tue Mar  3 19:10:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_30072.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_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/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_30072.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_30072.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_30072.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_2026/6m3w_30072.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.08, per 1000 atoms: 0.25
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  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: 0.61
  Conformation dependent library (CDL) restraints added in 360.6 milliseconds
  

  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: 0.24
  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: 1.13

  Time building geometry restraints manager: 0.84 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:
        0.00 -     2.10: 10494
        2.10 -     4.20: 743
        4.20 -     6.30: 178
        6.30 -     8.40: 12
        8.40 -    10.50: 21
  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 3.040
  nonbonded pdb=" O   GLY C1149 "
            pdb=" OG  SER C1152 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLY A1149 "
            pdb=" OG  SER A1152 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OD2 ASP A1145 "
            pdb=" OG  SER C 956 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   GLU B 918 "
            pdb=" OG1 THR B 922 "
     model   vdw
     2.293 3.040
  ... (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
Time spend for trying shortcut: 0.02
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:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.780
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.160
-------------------------------------------------------------------------------
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   8469  Z= 0.514
  Angle     :  1.369  14.712  11544  Z= 0.700
  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 : 9.66
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.011   0.002   ARG B1055 
 TYR   0.023   0.004   TYR B1029 
 PHE   0.038   0.006   PHE C 952 
 TRP   0.016   0.006   TRP B1084 
 HIS   0.006   0.002   HIS B1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.01096 ( 8433)
  covalent geometry    : angle       1.30693 (11448)
  SS BOND              : bond        0.00741 (   12)
  SS BOND              : angle       2.03832 (   24)
  hydrogen bonds       : bond        0.13763 (  471)
  hydrogen bonds       : angle       7.83782 ( 1422)
  link_NAG-ASN         : bond        0.01558 (   24)
  link_NAG-ASN         : angle       5.23566 (   72)

*********************** 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 to be fit.
    rotamer outliers: 6
    poor density    : 227
  time to evaluate  : 0.316 
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: 0.8299 (t80) cc_final: 0.7810 (t80)
REVERT: A 1070 TYR cc_start: 0.7321 (m-80) cc_final: 0.6847 (m-80)
REVERT: B  907 ASN cc_start: 0.7895 (m-40) cc_final: 0.7577 (p0)
REVERT: B  989 TYR cc_start: 0.8278 (t80) cc_final: 0.7906 (t80)
REVERT: C  907 ASN cc_start: 0.7801 (m-40) cc_final: 0.7354 (p0)
REVERT: C  976 ASP cc_start: 0.7539 (m-30) cc_final: 0.6591 (m-30)
REVERT: C  994 LEU cc_start: 0.9438 (mt) cc_final: 0.9209 (tp)
REVERT: C 1130 PHE cc_start: 0.8658 (m-80) cc_final: 0.8454 (m-80)
  outliers start: 6
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1057
  time to fit residues: 32.3882
Evaluate side-chains
  126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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
A1141 HIS
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1036 GLN
B1065 HIS
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 746 ASN
C 993 GLN
C1090 ASN
C1141 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.071747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.062278 restraints weight = 37979.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.063870 restraints weight = 22841.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.065001 restraints weight = 15807.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.065764 restraints weight = 12000.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.066325 restraints weight = 9724.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8469  Z= 0.179
  Angle     :  0.907   9.118  11544  Z= 0.422
  Chirality :  0.059   0.409   1419
  Planarity :  0.006   0.057   1461
  Dihedral  : 18.055  96.816   1590
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 11.52 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.23), residues: 1020
  helix:  0.08 (0.21), residues: 492
  sheet: -3.16 (0.43), residues: 117
  loop : -3.67 (0.23), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 977 
 TYR   0.015   0.001   TYR C 989 
 PHE   0.023   0.002   PHE B1079 
 TRP   0.004   0.001   TRP A1084 
 HIS   0.002   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8433)
  covalent geometry    : angle       0.86605 (11448)
  SS BOND              : bond        0.00509 (   12)
  SS BOND              : angle       1.19634 (   24)
  hydrogen bonds       : bond        0.05174 (  471)
  hydrogen bonds       : angle       5.71346 ( 1422)
  link_NAG-ASN         : bond        0.00960 (   24)
  link_NAG-ASN         : angle       3.47489 (   72)

*********************** 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
  196 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 160
  time to evaluate  : 0.343 
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: B  996 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7271 (tpt170)
REVERT: B 1131 LYS cc_start: 0.8326 (mmpt) cc_final: 0.7994 (mmtm)
REVERT: B 1166 ASP cc_start: 0.8039 (m-30) cc_final: 0.7652 (t0)
REVERT: C  976 ASP cc_start: 0.7492 (m-30) cc_final: 0.7203 (m-30)
REVERT: C  994 LEU cc_start: 0.9474 (mt) cc_final: 0.9265 (mt)
REVERT: C 1166 ASP cc_start: 0.8015 (m-30) cc_final: 0.7760 (t0)
  outliers start: 36
  outliers final: 15
  residues processed: 186
  average time/residue: 0.0910
  time to fit residues: 23.0026
Evaluate side-chains
  135 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1176 ASN
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 1176 ASN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  972 GLU
Chi-restraints excluded: chain C residue 1019 SER
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 907 ASN
** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 984 GLN
B1141 HIS
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.070416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.060708 restraints weight = 38286.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062268 restraints weight = 23404.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063352 restraints weight = 16421.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.064121 restraints weight = 12624.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.064668 restraints weight = 10283.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8469  Z= 0.210
  Angle     :  0.870   8.840  11544  Z= 0.407
  Chirality :  0.057   0.365   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 14.962  91.557   1590
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 12.96 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.24), residues: 1020
  helix:  0.60 (0.22), residues: 495
  sheet: -3.13 (0.42), residues: 117
  loop : -3.68 (0.24), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 977 
 TYR   0.012   0.002   TYR C 738 
 PHE   0.016   0.002   PHE B1057 
 TRP   0.004   0.001   TRP C1084 
 HIS   0.019   0.002   HIS B1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8433)
  covalent geometry    : angle       0.83189 (11448)
  SS BOND              : bond        0.00348 (   12)
  SS BOND              : angle       1.26841 (   24)
  hydrogen bonds       : bond        0.05161 (  471)
  hydrogen bonds       : angle       5.37209 ( 1422)
  link_NAG-ASN         : bond        0.00858 (   24)
  link_NAG-ASN         : angle       3.29567 (   72)

*********************** 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
  166 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 120
  time to evaluate  : 0.329 
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  936 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: A 1070 TYR cc_start: 0.7063 (m-80) cc_final: 0.6794 (m-80)
REVERT: B  976 ASP cc_start: 0.7831 (m-30) cc_final: 0.7434 (m-30)
REVERT: B  996 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7296 (tpp-160)
REVERT: B 1130 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.8009 (t80)
REVERT: B 1166 ASP cc_start: 0.8025 (m-30) cc_final: 0.7771 (t0)
REVERT: C  972 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7134 (mp0)
REVERT: C 1130 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8010 (t80)
REVERT: C 1166 ASP cc_start: 0.8038 (m-30) cc_final: 0.7837 (t0)
  outliers start: 46
  outliers final: 24
  residues processed: 154
  average time/residue: 0.1043
  time to fit residues: 21.5215
Evaluate side-chains
  130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 1045 LEU
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1126 GLU
Chi-restraints excluded: chain B residue  944 LEU
Chi-restraints excluded: chain B residue  948 LEU
Chi-restraints excluded: chain B residue  965 ARG
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  972 GLU
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1130 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 935 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1090 ASN
** 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**
** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 935 ASN
** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.070139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.060396 restraints weight = 39316.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.061956 restraints weight = 23858.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.063052 restraints weight = 16694.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.063796 restraints weight = 12782.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.064384 restraints weight = 10454.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8469  Z= 0.206
  Angle     :  0.844   8.827  11544  Z= 0.397
  Chirality :  0.056   0.364   1419
  Planarity :  0.005   0.048   1461
  Dihedral  : 13.786  87.733   1590
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 13.62 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.25), residues: 1020
  helix:  0.90 (0.22), residues: 492
  sheet: -2.95 (0.40), residues: 123
  loop : -3.76 (0.24), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 977 
 TYR   0.009   0.001   TYR B1120 
 PHE   0.015   0.002   PHE B1057 
 TRP   0.003   0.001   TRP C1084 
 HIS   0.004   0.001   HIS B1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 8433)
  covalent geometry    : angle       0.80560 (11448)
  SS BOND              : bond        0.00266 (   12)
  SS BOND              : angle       1.36884 (   24)
  hydrogen bonds       : bond        0.05118 (  471)
  hydrogen bonds       : angle       5.14725 ( 1422)
  link_NAG-ASN         : bond        0.00808 (   24)
  link_NAG-ASN         : angle       3.23034 (   72)

*********************** 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
  159 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 110
  time to evaluate  : 0.337 
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  936 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A 1070 TYR cc_start: 0.7197 (m-80) cc_final: 0.6875 (m-80)
REVERT: B  976 ASP cc_start: 0.7918 (m-30) cc_final: 0.6723 (m-30)
REVERT: B 1020 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8702 (mtpp)
REVERT: C  976 ASP cc_start: 0.7626 (m-30) cc_final: 0.6885 (m-30)
REVERT: C  977 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8116 (mtt90)
REVERT: C 1130 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8221 (t80)
  outliers start: 49
  outliers final: 34
  residues processed: 146
  average time/residue: 0.0971
  time to fit residues: 19.3648
Evaluate side-chains
  132 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
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  994 LEU
Chi-restraints excluded: chain A residue 1045 LEU
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  725 CYS
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 1020 LYS
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 1092 PHE
Chi-restraints excluded: chain B residue 1176 ASN
Chi-restraints excluded: chain C residue  725 CYS
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  986 LEU
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1020 LYS
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1092 PHE
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 79 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.070087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.060316 restraints weight = 39466.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.061857 restraints weight = 24208.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062924 restraints weight = 17027.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.063659 restraints weight = 13111.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.064223 restraints weight = 10804.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8469  Z= 0.197
  Angle     :  0.805   8.756  11544  Z= 0.380
  Chirality :  0.054   0.356   1419
  Planarity :  0.005   0.047   1461
  Dihedral  : 13.033  84.280   1590
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 15.61 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.24), residues: 1020
  helix:  1.02 (0.22), residues: 495
  sheet: -2.85 (0.38), residues: 132
  loop : -3.95 (0.22), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 977 
 TYR   0.009   0.001   TYR A 989 
 PHE   0.015   0.002   PHE C 741 
 TRP   0.003   0.001   TRP B1084 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8433)
  covalent geometry    : angle       0.76676 (11448)
  SS BOND              : bond        0.00274 (   12)
  SS BOND              : angle       1.42512 (   24)
  hydrogen bonds       : bond        0.05026 (  471)
  hydrogen bonds       : angle       4.97137 ( 1422)
  link_NAG-ASN         : bond        0.00769 (   24)
  link_NAG-ASN         : angle       3.12889 (   72)

*********************** 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
  149 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 104
  time to evaluate  : 0.301 
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 1070 TYR cc_start: 0.7184 (m-80) cc_final: 0.6853 (m-80)
REVERT: C  976 ASP cc_start: 0.7555 (m-30) cc_final: 0.6914 (m-30)
REVERT: C 1011 MET cc_start: 0.8496 (ppp) cc_final: 0.8009 (ppp)
  outliers start: 45
  outliers final: 36
  residues processed: 135
  average time/residue: 0.0959
  time to fit residues: 17.3466
Evaluate side-chains
  127 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
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  994 LEU
Chi-restraints excluded: chain A residue 1045 LEU
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  725 CYS
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  990 VAL
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1071 PHE
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  944 LEU
Chi-restraints excluded: chain C residue  949 SER
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 1092 PHE
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1126 GLU
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 26 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0020
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 84 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.7990

-------------------------------------------------------------------------------
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 942 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 = 0.3546 r_free = 0.3546 target = 0.070871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.061097 restraints weight = 38629.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.062678 restraints weight = 23618.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063800 restraints weight = 16506.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.064564 restraints weight = 12612.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.065126 restraints weight = 10314.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8469  Z= 0.164
  Angle     :  0.774   8.687  11544  Z= 0.368
  Chirality :  0.053   0.346   1419
  Planarity :  0.005   0.043   1461
  Dihedral  : 12.398  81.546   1590
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.72 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.24), residues: 1020
  helix:  1.12 (0.22), residues: 495
  sheet: -2.84 (0.39), residues: 126
  loop : -3.88 (0.22), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 977 
 TYR   0.008   0.001   TYR A1049 
 PHE   0.013   0.002   PHE C 741 
 TRP   0.003   0.001   TRP B1084 
 HIS   0.003   0.001   HIS A1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8433)
  covalent geometry    : angle       0.73741 (11448)
  SS BOND              : bond        0.00237 (   12)
  SS BOND              : angle       1.15772 (   24)
  hydrogen bonds       : bond        0.04791 (  471)
  hydrogen bonds       : angle       4.81220 ( 1422)
  link_NAG-ASN         : bond        0.00723 (   24)
  link_NAG-ASN         : angle       3.02457 (   72)

*********************** 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
  145 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 0.317 
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: B 1011 MET cc_start: 0.8153 (ppp) cc_final: 0.7615 (ppp)
REVERT: C  976 ASP cc_start: 0.7553 (m-30) cc_final: 0.6914 (m-30)
REVERT: C  977 ARG cc_start: 0.8606 (mtt90) cc_final: 0.8312 (mtt90)
REVERT: C 1011 MET cc_start: 0.8472 (ppp) cc_final: 0.8028 (ppp)
  outliers start: 35
  outliers final: 28
  residues processed: 135
  average time/residue: 0.0946
  time to fit residues: 17.1799
Evaluate side-chains
  124 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue  994 LEU
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
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  725 CYS
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 1092 PHE
Chi-restraints excluded: chain C residue  725 CYS
Chi-restraints excluded: chain C residue  944 LEU
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 1092 PHE
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 72 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 936 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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.070518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.060822 restraints weight = 38640.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062347 restraints weight = 24092.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.063413 restraints weight = 17115.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.064176 restraints weight = 13277.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.064712 restraints weight = 10898.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8469  Z= 0.171
  Angle     :  0.775  10.143  11544  Z= 0.369
  Chirality :  0.052   0.332   1419
  Planarity :  0.005   0.044   1461
  Dihedral  : 11.959  78.671   1590
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.16 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.24), residues: 1020
  helix:  1.19 (0.22), residues: 498
  sheet: -2.77 (0.40), residues: 126
  loop : -3.91 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 977 
 TYR   0.009   0.001   TYR B1120 
 PHE   0.012   0.002   PHE C1057 
 TRP   0.002   0.001   TRP B1084 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8433)
  covalent geometry    : angle       0.73982 (11448)
  SS BOND              : bond        0.00299 (   12)
  SS BOND              : angle       1.51498 (   24)
  hydrogen bonds       : bond        0.04778 (  471)
  hydrogen bonds       : angle       4.73350 ( 1422)
  link_NAG-ASN         : bond        0.00673 (   24)
  link_NAG-ASN         : angle       2.93375 (   72)

*********************** 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
  141 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 0.381 
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: A  936 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B 1011 MET cc_start: 0.8180 (ppp) cc_final: 0.7678 (ppp)
REVERT: B 1014 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7075 (m)
REVERT: C  976 ASP cc_start: 0.7537 (m-30) cc_final: 0.7030 (m-30)
REVERT: C  977 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8279 (mtt90)
REVERT: C 1011 MET cc_start: 0.8408 (ppp) cc_final: 0.7976 (ppp)
  outliers start: 40
  outliers final: 31
  residues processed: 130
  average time/residue: 0.1049
  time to fit residues: 18.4281
Evaluate side-chains
  125 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
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  994 LEU
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  725 CYS
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 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 C residue  725 CYS
Chi-restraints excluded: chain C residue  944 LEU
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 1045 LEU
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1126 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 936 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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.070591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.061010 restraints weight = 37967.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062558 restraints weight = 23677.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063601 restraints weight = 16754.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.064388 restraints weight = 12932.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.064839 restraints weight = 10590.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8469  Z= 0.178
  Angle     :  0.762  11.069  11544  Z= 0.365
  Chirality :  0.052   0.316   1419
  Planarity :  0.005   0.044   1461
  Dihedral  : 11.549  75.639   1590
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 18.16 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.24), residues: 1020
  helix:  1.24 (0.21), residues: 498
  sheet: -2.73 (0.40), residues: 126
  loop : -3.88 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 977 
 TYR   0.010   0.001   TYR B 738 
 PHE   0.014   0.002   PHE B 741 
 TRP   0.002   0.001   TRP B1084 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8433)
  covalent geometry    : angle       0.72862 (11448)
  SS BOND              : bond        0.00242 (   12)
  SS BOND              : angle       1.29481 (   24)
  hydrogen bonds       : bond        0.04746 (  471)
  hydrogen bonds       : angle       4.72463 ( 1422)
  link_NAG-ASN         : bond        0.00683 (   24)
  link_NAG-ASN         : angle       2.86626 (   72)

*********************** 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
  146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 99
  time to evaluate  : 0.373 
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: A  936 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: B  744 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6098 (tt0)
REVERT: B 1011 MET cc_start: 0.8259 (ppp) cc_final: 0.7768 (ppp)
REVERT: B 1014 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7143 (m)
REVERT: C  976 ASP cc_start: 0.7548 (m-30) cc_final: 0.7108 (m-30)
REVERT: C  977 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8279 (mtt90)
REVERT: C 1011 MET cc_start: 0.8473 (ppp) cc_final: 0.8059 (ppp)
  outliers start: 47
  outliers final: 35
  residues processed: 133
  average time/residue: 0.1056
  time to fit residues: 18.8864
Evaluate side-chains
  129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 92
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
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  994 LEU
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  725 CYS
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  744 GLN
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 1014 CYS
Chi-restraints excluded: chain B residue 1065 HIS
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1087 THR
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  725 CYS
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  949 SER
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 1045 LEU
Chi-restraints excluded: chain C residue 1071 PHE
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 1112 ILE
Chi-restraints excluded: chain C residue 1126 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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**
** 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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 936 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**
** C1101 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 = 0.3527 r_free = 0.3527 target = 0.069621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.059976 restraints weight = 38308.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.061522 restraints weight = 23756.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.062595 restraints weight = 16719.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.063373 restraints weight = 12856.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.063905 restraints weight = 10516.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8469  Z= 0.214
  Angle     :  0.794  12.865  11544  Z= 0.383
  Chirality :  0.052   0.292   1419
  Planarity :  0.005   0.049   1461
  Dihedral  : 11.229  72.340   1590
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 18.27 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.24), residues: 1020
  helix:  1.12 (0.21), residues: 498
  sheet: -2.66 (0.40), residues: 126
  loop : -3.81 (0.23), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 977 
 TYR   0.009   0.001   TYR B1120 
 PHE   0.015   0.002   PHE C1057 
 TRP   0.005   0.002   TRP C1084 
 HIS   0.005   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8433)
  covalent geometry    : angle       0.76222 (11448)
  SS BOND              : bond        0.00359 (   12)
  SS BOND              : angle       1.52859 (   24)
  hydrogen bonds       : bond        0.04946 (  471)
  hydrogen bonds       : angle       4.87356 ( 1422)
  link_NAG-ASN         : bond        0.00677 (   24)
  link_NAG-ASN         : angle       2.82923 (   72)

*********************** 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
  140 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 91
  time to evaluate  : 0.304 
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 1070 TYR cc_start: 0.7294 (m-80) cc_final: 0.6894 (m-80)
REVERT: B  744 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6343 (tt0)
REVERT: B 1011 MET cc_start: 0.8338 (ppp) cc_final: 0.7825 (ppp)
REVERT: B 1014 CYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7160 (m)
REVERT: C  976 ASP cc_start: 0.7578 (m-30) cc_final: 0.7192 (m-30)
REVERT: C  977 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8357 (mtt90)
REVERT: C 1011 MET cc_start: 0.8537 (ppp) cc_final: 0.8096 (ppp)
REVERT: C 1126 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.5175 (pp20)
  outliers start: 49
  outliers final: 39
  residues processed: 126
  average time/residue: 0.1097
  time to fit residues: 18.5167
Evaluate side-chains
  130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 88
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  731 CYS
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  994 LEU
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain B residue  725 CYS
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  744 GLN
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  988 THR
Chi-restraints excluded: chain B residue  990 VAL
Chi-restraints excluded: chain B residue 1014 CYS
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 1087 THR
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain C residue  725 CYS
Chi-restraints excluded: chain C residue  744 GLN
Chi-restraints excluded: chain C residue  944 LEU
Chi-restraints excluded: chain C residue  949 SER
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 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 1126 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 62 optimal weight:    0.2980
   chunk 78 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
A1036 GLN
** 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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 936 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**
** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.071423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.061821 restraints weight = 37872.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.063391 restraints weight = 23488.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.064480 restraints weight = 16607.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065212 restraints weight = 12734.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.065832 restraints weight = 10454.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8469  Z= 0.151
  Angle     :  0.751  14.534  11544  Z= 0.358
  Chirality :  0.052   0.306   1419
  Planarity :  0.005   0.044   1461
  Dihedral  : 10.751  69.868   1590
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.71 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.25), residues: 1020
  helix:  1.37 (0.22), residues: 498
  sheet: -2.87 (0.37), residues: 156
  loop : -3.89 (0.23), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C1073 
 TYR   0.010   0.001   TYR C1029 
 PHE   0.015   0.002   PHE B 741 
 TRP   0.006   0.001   TRP B1084 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8433)
  covalent geometry    : angle       0.71780 (11448)
  SS BOND              : bond        0.00215 (   12)
  SS BOND              : angle       1.23909 (   24)
  hydrogen bonds       : bond        0.04600 (  471)
  hydrogen bonds       : angle       4.62714 ( 1422)
  link_NAG-ASN         : bond        0.00660 (   24)
  link_NAG-ASN         : angle       2.84148 (   72)

********************** 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
  139 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.332 
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: B  702 ILE cc_start: 0.9229 (mm) cc_final: 0.8994 (tt)
REVERT: B  744 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6241 (tt0)
REVERT: B 1011 MET cc_start: 0.8241 (ppp) cc_final: 0.7722 (ppp)
REVERT: B 1014 CYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7172 (m)
REVERT: C  976 ASP cc_start: 0.7525 (m-30) cc_final: 0.7295 (m-30)
REVERT: C  977 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8317 (mtt90)
REVERT: C 1011 MET cc_start: 0.8516 (ppp) cc_final: 0.8109 (ppp)
REVERT: C 1090 ASN cc_start: 0.8962 (m-40) cc_final: 0.8737 (t0)
  outliers start: 35
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1004
  time to fit residues: 17.4403
Evaluate side-chains
  122 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue  994 LEU
Chi-restraints excluded: chain A residue 1014 CYS
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain B residue  725 CYS
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  744 GLN
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  988 THR
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 1126 GLU
Chi-restraints excluded: chain C residue  725 CYS
Chi-restraints excluded: chain C residue  744 GLN
Chi-restraints excluded: chain C residue  949 SER
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 1045 LEU
Chi-restraints excluded: chain C residue 1076 VAL
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1126 GLU
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 55 optimal weight:    0.0980
   chunk 100 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 984 GLN ** 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**
** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 936 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**
** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.071916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.062193 restraints weight = 37829.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063749 restraints weight = 23782.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.064737 restraints weight = 16959.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.065548 restraints weight = 13374.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.066024 restraints weight = 10992.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8469  Z= 0.151
  Angle     :  0.750  15.076  11544  Z= 0.357
  Chirality :  0.051   0.296   1419
  Planarity :  0.005   0.044   1461
  Dihedral  : 10.429  66.237   1590
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 19.82 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.25), residues: 1020
  helix:  1.48 (0.22), residues: 498
  sheet: -2.47 (0.42), residues: 126
  loop : -3.67 (0.24), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1073 
 TYR   0.013   0.001   TYR C1029 
 PHE   0.014   0.002   PHE A 909 
 TRP   0.003   0.001   TRP B1084 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8433)
  covalent geometry    : angle       0.71696 (11448)
  SS BOND              : bond        0.00195 (   12)
  SS BOND              : angle       1.39420 (   24)
  hydrogen bonds       : bond        0.04621 (  471)
  hydrogen bonds       : angle       4.49344 ( 1422)
  link_NAG-ASN         : bond        0.00668 (   24)
  link_NAG-ASN         : angle       2.79250 (   72)

===============================================================================
Job complete
usr+sys time: 1349.90 seconds
wall clock time: 24 minutes 16.32 seconds (1456.32 seconds total)