Starting phenix.real_space_refine
on Fri Sep 11 17:51:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11sm_76007/09_2026/11sm_76007.cif"
  }
  resolution = 3.4
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 sd=   0.282
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      35      5.16       5
     C    6622      2.51       5
     N    1750      2.21       5
     O    1848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10255
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1465
          Classifications: {'peptide': 187}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 2.46, per 1000 atoms: 0.24
  Number of scatterers: 10255
  At special positions: 0
  Unit cell: (100.793, 99.099, 101.64, 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      35     16.00
     O    1848      8.00
     N    1750      7.00
     C    6622      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 351.9 milliseconds
  

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2464

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      37.3% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 901 through 912
      removed outlier: 4.127A  pdb=" N   ALA A 905 " --> pdb=" O   GLN A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 931
      removed outlier: 3.504A  pdb=" N   PHE A 919 " --> pdb=" O   LEU A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 975
    Processing helix  chain 'A' and resid 1002 through 1017
      removed outlier: 4.144A  pdb=" N   CYS A1017 " --> pdb=" O   ALA A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1070
      removed outlier: 3.617A  pdb=" N   LEU A1055 " --> pdb=" O   HIS A1051 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 901 through 912
      removed outlier: 4.254A  pdb=" N   ALA B 905 " --> pdb=" O   GLN B 901 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 915 through 932
      removed outlier: 3.623A  pdb=" N   PHE B 919 " --> pdb=" O   LEU B 915 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 975
    Processing helix  chain 'B' and resid 1002 through 1017
      removed outlier: 4.179A  pdb=" N   CYS B1017 " --> pdb=" O   ALA B1013 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1051 through 1070
      removed outlier: 3.590A  pdb=" N   LEU B1055 " --> pdb=" O   HIS B1051 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 902 through 912
    Processing helix  chain 'C' and resid 915 through 932
      removed outlier: 3.534A  pdb=" N   PHE C 919 " --> pdb=" O   LEU C 915 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 972 through 975
    Processing helix  chain 'C' and resid 1002 through 1017
      removed outlier: 4.135A  pdb=" N   CYS C1017 " --> pdb=" O   ALA C1013 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1051 through 1070
      removed outlier: 3.522A  pdb=" N   LEU C1055 " --> pdb=" O   HIS C1051 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 901 through 912
      removed outlier: 4.250A  pdb=" N   ALA D 905 " --> pdb=" O   GLN D 901 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 915 through 932
      removed outlier: 3.553A  pdb=" N   PHE D 919 " --> pdb=" O   LEU D 915 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 972 through 975
    Processing helix  chain 'D' and resid 1002 through 1017
      removed outlier: 4.237A  pdb=" N   CYS D1017 " --> pdb=" O   ALA D1013 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1051 through 1070
    Processing helix  chain 'E' and resid 900 through 912
      removed outlier: 3.990A  pdb=" N   VAL E 904 " --> pdb=" O   LEU E 900 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ALA E 905 " --> pdb=" O   GLN E 901 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 915 through 932
    Processing helix  chain 'E' and resid 972 through 975
    Processing helix  chain 'E' and resid 1002 through 1017
      removed outlier: 4.157A  pdb=" N   CYS E1017 " --> pdb=" O   ALA E1013 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1051 through 1070
    Processing helix  chain 'F' and resid 901 through 912
      removed outlier: 4.318A  pdb=" N   ALA F 905 " --> pdb=" O   GLN F 901 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 915 through 931
    Processing helix  chain 'F' and resid 972 through 975
    Processing helix  chain 'F' and resid 1002 through 1017
      removed outlier: 4.242A  pdb=" N   CYS F1017 " --> pdb=" O   ALA F1013 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1051 through 1070
      removed outlier: 3.579A  pdb=" N   LEU F1055 " --> pdb=" O   HIS F1051 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 901 through 912
      removed outlier: 4.231A  pdb=" N   ALA G 905 " --> pdb=" O   GLN G 901 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 915 through 932
    Processing helix  chain 'G' and resid 972 through 975
    Processing helix  chain 'G' and resid 1002 through 1017
      removed outlier: 4.163A  pdb=" N   CYS G1017 " --> pdb=" O   ALA G1013 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1051 through 1070
      removed outlier: 3.580A  pdb=" N   LEU G1055 " --> pdb=" O   HIS G1051 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 939 through 941
      removed outlier: 7.035A  pdb=" N   THR A 958 " --> pdb=" O   THR A 950 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ILE A 952 " --> pdb=" O   ALA A 956 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA A 956 " --> pdb=" O   ILE A 952 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLU A 966 " --> pdb=" O   ASN B 981 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR B 958 " --> pdb=" O   THR B 950 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   ILE B 952 " --> pdb=" O   ALA B 956 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ALA B 956 " --> pdb=" O   ILE B 952 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU B 966 " --> pdb=" O   ASN C 981 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   THR C 958 " --> pdb=" O   THR C 950 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ILE C 952 " --> pdb=" O   ALA C 956 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ALA C 956 " --> pdb=" O   ILE C 952 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   GLU C 966 " --> pdb=" O   ASN D 981 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY D 947 " --> pdb=" O   VAL D 940 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   THR D 958 " --> pdb=" O   THR D 950 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   ILE D 952 " --> pdb=" O   ALA D 956 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ALA D 956 " --> pdb=" O   ILE D 952 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU D 966 " --> pdb=" O   ASN E 981 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   THR E 958 " --> pdb=" O   THR E 950 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ILE E 952 " --> pdb=" O   ALA E 956 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ALA E 956 " --> pdb=" O   ILE E 952 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLU E 966 " --> pdb=" O   ASN F 981 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   THR F 958 " --> pdb=" O   THR F 950 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   ILE F 952 " --> pdb=" O   ALA F 956 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ALA F 956 " --> pdb=" O   ILE F 952 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLU F 966 " --> pdb=" O   ASN G 981 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR G 958 " --> pdb=" O   THR G 950 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ILE G 952 " --> pdb=" O   ALA G 956 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ALA G 956 " --> pdb=" O   ILE G 952 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU G 966 " --> pdb=" O   ASN A 981 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 990 through 997
      removed outlier: 6.792A  pdb=" N   ILE A1039 " --> pdb=" O   VAL A1031 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU A1027 " --> pdb=" O   ARG A1043 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 990 through 997
      removed outlier: 6.934A  pdb=" N   ILE B1039 " --> pdb=" O   VAL B1031 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU B1027 " --> pdb=" O   ARG B1043 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 990 through 997
      removed outlier: 6.908A  pdb=" N   ILE C1039 " --> pdb=" O   VAL C1031 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU C1027 " --> pdb=" O   ARG C1043 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1078 through 1081
    Processing sheet with id=AA6, first strand: chain 'D' and resid 990 through 997
      removed outlier: 3.710A  pdb=" N   ASP D1032 " --> pdb=" O   ILE D1039 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   GLU D1041 " --> pdb=" O   LEU D1030 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   LEU D1030 " --> pdb=" O   GLU D1041 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   ARG D1043 " --> pdb=" O   VAL D1028 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL D1028 " --> pdb=" O   ARG D1043 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 990 through 997
      removed outlier: 3.756A  pdb=" N   ASP E1032 " --> pdb=" O   ILE E1039 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   GLU E1041 " --> pdb=" O   LEU E1030 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   LEU E1030 " --> pdb=" O   GLU E1041 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   ARG E1043 " --> pdb=" O   VAL E1028 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL E1028 " --> pdb=" O   ARG E1043 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 990 through 997
      removed outlier: 6.980A  pdb=" N   ILE F1039 " --> pdb=" O   VAL F1031 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU F1027 " --> pdb=" O   ARG F1043 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 1078 through 1081
    Processing sheet with id=AB1, first strand: chain 'G' and resid 990 through 997
      removed outlier: 6.953A  pdb=" N   ILE G1039 " --> pdb=" O   VAL G1031 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU G1027 " --> pdb=" O   ARG G1043 " (cutoff:3.500A)

    516 hydrogen bonds defined for protein.
    1467 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: 1.32

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3376
        1.34 -     1.46: 1992
        1.46 -     1.58: 5041
        1.58 -     1.69: 7
        1.69 -     1.81: 63
  Bond restraints: 10479
  Sorted by residual:
  bond pdb=" CB  PRO F1075 "
       pdb=" CG  PRO F1075 "
    ideal  model  delta    sigma   weight residual
    1.492  1.601 -0.109 5.00e-02 4.00e+02 4.79e+00
  bond pdb=" CB  PRO D1075 "
       pdb=" CG  PRO D1075 "
    ideal  model  delta    sigma   weight residual
    1.492  1.599 -0.107 5.00e-02 4.00e+02 4.57e+00
  bond pdb=" CB  PRO B1075 "
       pdb=" CG  PRO B1075 "
    ideal  model  delta    sigma   weight residual
    1.492  1.596 -0.104 5.00e-02 4.00e+02 4.29e+00
  bond pdb=" CB  PRO E1075 "
       pdb=" CG  PRO E1075 "
    ideal  model  delta    sigma   weight residual
    1.492  1.592 -0.100 5.00e-02 4.00e+02 4.00e+00
  bond pdb=" CB  PRO C1075 "
       pdb=" CG  PRO C1075 "
    ideal  model  delta    sigma   weight residual
    1.492  1.584 -0.092 5.00e-02 4.00e+02 3.36e+00
  ... (remaining 10474 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 14067
        2.83 -     5.65: 175
        5.65 -     8.48: 10
        8.48 -    11.30: 10
       11.30 -    14.13: 4
  Bond angle restraints: 14266
  Sorted by residual:
  angle pdb=" CA  PRO F1075 "
        pdb=" N   PRO F1075 "
        pdb=" CD  PRO F1075 "
      ideal   model   delta    sigma   weight residual
     112.00  102.63    9.37 1.40e+00 5.10e-01 4.48e+01
  angle pdb=" CA  PRO D1075 "
        pdb=" N   PRO D1075 "
        pdb=" CD  PRO D1075 "
      ideal   model   delta    sigma   weight residual
     112.00  102.73    9.27 1.40e+00 5.10e-01 4.38e+01
  angle pdb=" CA  PRO B1075 "
        pdb=" N   PRO B1075 "
        pdb=" CD  PRO B1075 "
      ideal   model   delta    sigma   weight residual
     112.00  103.37    8.63 1.40e+00 5.10e-01 3.80e+01
  angle pdb=" CA  PRO E1075 "
        pdb=" N   PRO E1075 "
        pdb=" CD  PRO E1075 "
      ideal   model   delta    sigma   weight residual
     112.00  103.60    8.40 1.40e+00 5.10e-01 3.60e+01
  angle pdb=" CA  PRO G1075 "
        pdb=" N   PRO G1075 "
        pdb=" CD  PRO G1075 "
      ideal   model   delta    sigma   weight residual
     112.00  103.85    8.15 1.40e+00 5.10e-01 3.39e+01
  ... (remaining 14261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5270
       17.97 -    35.94: 752
       35.94 -    53.91: 190
       53.91 -    71.89: 42
       71.89 -    89.86: 11
  Dihedral angle restraints: 6265
    sinusoidal: 2492
      harmonic: 3773
  Sorted by residual:
  dihedral pdb=" CA  TRP A 962 "
           pdb=" C   TRP A 962 "
           pdb=" N   ASP A 963 "
           pdb=" CA  ASP A 963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.87   23.13     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  TRP E 962 "
           pdb=" C   TRP E 962 "
           pdb=" N   ASP E 963 "
           pdb=" CA  ASP E 963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.75   22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  TRP G 962 "
           pdb=" C   TRP G 962 "
           pdb=" N   ASP G 963 "
           pdb=" CA  ASP G 963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1008
       0.033 -    0.066: 366
       0.066 -    0.099: 185
       0.099 -    0.132: 118
       0.132 -    0.165: 10
  Chirality restraints: 1687
  Sorted by residual:
  chirality pdb=" CA  ASP C 961 "
            pdb=" N   ASP C 961 "
            pdb=" C   ASP C 961 "
            pdb=" CB  ASP C 961 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  ASP G 961 "
            pdb=" N   ASP G 961 "
            pdb=" C   ASP G 961 "
            pdb=" CB  ASP G 961 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  MET A1053 "
            pdb=" N   MET A1053 "
            pdb=" C   MET A1053 "
            pdb=" CB  MET A1053 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.79e-01
  ... (remaining 1684 not shown)

  Planarity restraints: 1827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET F1074 "    0.082 5.00e-02 4.00e+02   1.19e-01 2.27e+01
        pdb=" N   PRO F1075 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO F1075 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO F1075 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D1074 "    0.081 5.00e-02 4.00e+02   1.18e-01 2.21e+01
        pdb=" N   PRO D1075 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO D1075 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO D1075 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B1074 "    0.080 5.00e-02 4.00e+02   1.17e-01 2.17e+01
        pdb=" N   PRO B1075 "   -0.201 5.00e-02 4.00e+02
        pdb=" CA  PRO B1075 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO B1075 "    0.061 5.00e-02 4.00e+02
  ... (remaining 1824 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2610
        2.80 -     3.33: 9534
        3.33 -     3.85: 16283
        3.85 -     4.38: 17394
        4.38 -     4.90: 31512
  Nonbonded interactions: 77333
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 988 "
            pdb=" OG1 THR D 989 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OE1 GLU A1041 "
            pdb=" NH1 ARG A1043 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" N   GLN E 916 "
            pdb=" OE1 GLN E 916 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" NE2 GLN E1080 "
            pdb=" OE2 GLU F1084 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" N   GLU E 977 "
            pdb=" OE1 GLU E 977 "
     model   vdw
     2.360 3.120
  ... (remaining 77328 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             7.420
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     10.390
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  10479  Z= 0.147
  Angle     :  0.792  14.130  14266  Z= 0.404
  Chirality :  0.049   0.165   1687
  Planarity :  0.008   0.119   1827
  Dihedral  : 18.146  89.857   3801
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.54 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 31.01 %
    Favored  : 68.08 %
  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: -0.30 (0.24), residues: 1295
  helix:  2.15 (0.25), residues: 420
  sheet:  0.44 (0.31), residues: 231
  loop : -2.21 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1052 
 TYR   0.002   0.000   TYR A1045 
 PHE   0.022   0.001   PHE D 913 
 TRP   0.009   0.001   TRP D 902 
 HIS   0.003   0.001   HIS C1051 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.15 (10479)
  covalent geometry    : angle       0.79230 /  0.40 (14266)
  hydrogen bonds       : bond        0.19963 / 13.07 (  516)
  hydrogen bonds       : angle       7.18392 /  5.00 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 298
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  913 PHE cc_start: 0.8212 (t80) cc_final: 0.7979 (t80)
REVERT: B  953 ASN cc_start: 0.8795 (t0) cc_final: 0.8075 (m-40)
REVERT: C  965 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7455 (ttmm)
REVERT: C  977 GLU cc_start: 0.7406 (mp0) cc_final: 0.6925 (mp0)
REVERT: C 1081 MET cc_start: 0.8098 (mmt) cc_final: 0.7000 (mpp)
REVERT: D  902 TRP cc_start: 0.7442 (m100) cc_final: 0.7167 (m100)
REVERT: D  953 ASN cc_start: 0.8750 (t0) cc_final: 0.8331 (m-40)
REVERT: E  953 ASN cc_start: 0.8882 (t0) cc_final: 0.8274 (m-40)
REVERT: F  907 LEU cc_start: 0.8484 (mt) cc_final: 0.8124 (pp)
REVERT: F 1081 MET cc_start: 0.8446 (mmp) cc_final: 0.8109 (mmp)
REVERT: G  977 GLU cc_start: 0.7410 (mp0) cc_final: 0.7039 (mp0)
  outliers start: 10
  outliers final: 2
  residues processed: 301
  average time/residue: 0.1274
  time to fit residues: 49.7883
Evaluate side-chains
  263 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 261
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 1038 GLN
Chi-restraints excluded: chain F residue  958 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 978 GLN
A1038 GLN
A1061 GLN
A1070 HIS
B1061 GLN
B1070 HIS
C1061 GLN
C1070 HIS
D1061 GLN
D1070 HIS
E1061 GLN
E1070 HIS
F1061 GLN
F1070 HIS
G1061 GLN
G1070 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.073808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.063080 restraints weight = 31059.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.04
r_work: 0.2898 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10479  Z= 0.157
  Angle     :  0.736  10.746  14266  Z= 0.373
  Chirality :  0.051   0.141   1687
  Planarity :  0.005   0.038   1827
  Dihedral  :  5.019  27.851   1390
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.72 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.39 %
    Favored  : 67.54 %
  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: -0.16 (0.24), residues: 1295
  helix:  2.16 (0.25), residues: 434
  sheet:  1.14 (0.31), residues: 224
  loop : -2.39 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E1016 
 TYR   0.009   0.001   TYR A1045 
 PHE   0.016   0.002   PHE G 919 
 TRP   0.015   0.001   TRP C 902 
 HIS   0.005   0.001   HIS C1051 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 (10479)
  covalent geometry    : angle       0.73614 /  0.37 (14266)
  hydrogen bonds       : bond        0.04603 /  3.08 (  516)
  hydrogen bonds       : angle       5.25755 /  3.67 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 305
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1034 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8753 (pt0)
REVERT: B  953 ASN cc_start: 0.8743 (t0) cc_final: 0.8536 (m-40)
REVERT: B  961 ASP cc_start: 0.7747 (p0) cc_final: 0.7454 (p0)
REVERT: B 1048 GLU cc_start: 0.8289 (pm20) cc_final: 0.8047 (pm20)
REVERT: B 1081 MET cc_start: 0.8706 (tpp) cc_final: 0.8260 (tpp)
REVERT: C  965 LYS cc_start: 0.8276 (ttmt) cc_final: 0.8035 (ttmm)
REVERT: C  982 TRP cc_start: 0.8493 (m100) cc_final: 0.8228 (m100)
REVERT: D  907 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8023 (pp)
REVERT: F  907 LEU cc_start: 0.8240 (mt) cc_final: 0.8033 (pp)
REVERT: G  907 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8174 (pp)
  outliers start: 45
  outliers final: 12
  residues processed: 325
  average time/residue: 0.1274
  time to fit residues: 54.0709
Evaluate side-chains
  279 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 264
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  963 ASP
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  915 LEU
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue 1017 CYS
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  989 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0570
   chunk 46 optimal weight:    0.5980
   chunk 120 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1061 GLN
A1070 HIS
B1070 HIS
C1061 GLN
C1070 HIS
D1061 GLN
D1070 HIS
E1070 HIS
F1061 GLN
F1070 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.071767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.061014 restraints weight = 30932.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.08
r_work: 0.2844 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10479  Z= 0.147
  Angle     :  0.716  10.222  14266  Z= 0.360
  Chirality :  0.050   0.142   1687
  Planarity :  0.005   0.042   1827
  Dihedral  :  4.903  25.060   1387
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.25 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 28.48 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.00 (0.24), residues: 1295
  helix:  2.27 (0.25), residues: 441
  sheet:  1.30 (0.31), residues: 224
  loop : -2.36 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F1016 
 TYR   0.004   0.001   TYR G1045 
 PHE   0.014   0.001   PHE C 919 
 TRP   0.013   0.001   TRP C 962 
 HIS   0.003   0.001   HIS F1057 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (10479)
  covalent geometry    : angle       0.71607 /  0.36 (14266)
  hydrogen bonds       : bond        0.04367 /  2.90 (  516)
  hydrogen bonds       : angle       4.82666 /  3.38 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 277
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  953 ASN cc_start: 0.8793 (t0) cc_final: 0.8571 (t0)
REVERT: A 1034 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8779 (pt0)
REVERT: A 1081 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7563 (mpp)
REVERT: B  907 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (pp)
REVERT: B  913 PHE cc_start: 0.8085 (t80) cc_final: 0.7574 (t80)
REVERT: B  916 GLN cc_start: 0.7602 (pm20) cc_final: 0.7255 (pm20)
REVERT: B  953 ASN cc_start: 0.8745 (t0) cc_final: 0.8497 (m-40)
REVERT: B  961 ASP cc_start: 0.7573 (p0) cc_final: 0.7183 (p0)
REVERT: C  965 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8053 (ttmm)
REVERT: D  907 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8046 (pp)
REVERT: D  977 GLU cc_start: 0.8070 (mp0) cc_final: 0.7833 (mp0)
REVERT: F  907 LEU cc_start: 0.8353 (mt) cc_final: 0.8132 (pp)
REVERT: F  951 LYS cc_start: 0.9131 (tptm) cc_final: 0.8861 (tttp)
REVERT: G  907 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8149 (pp)
  outliers start: 52
  outliers final: 36
  residues processed: 302
  average time/residue: 0.1148
  time to fit residues: 46.3368
Evaluate side-chains
  313 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 272
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  945 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1070 HIS
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  963 ASP
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue  989 THR
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue 1017 CYS
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  915 LEU
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 96 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B1070 HIS
C1070 HIS
D1070 HIS
E 953 ASN
E1002 ASN
E1061 GLN
E1070 HIS
F1070 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.060397 restraints weight = 30927.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.00
r_work: 0.2831 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10479  Z= 0.161
  Angle     :  0.721  10.040  14266  Z= 0.367
  Chirality :  0.050   0.148   1687
  Planarity :  0.005   0.041   1827
  Dihedral  :  4.991  26.506   1387
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 28.30 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.05 (0.24), residues: 1295
  helix:  2.31 (0.25), residues: 441
  sheet:  1.44 (0.32), residues: 224
  loop : -2.37 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 990 
 TYR   0.005   0.001   TYR G1045 
 PHE   0.014   0.002   PHE C 919 
 TRP   0.027   0.002   TRP B 962 
 HIS   0.012   0.002   HIS B1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 (10479)
  covalent geometry    : angle       0.72147 /  0.37 (14266)
  hydrogen bonds       : bond        0.04270 /  2.84 (  516)
  hydrogen bonds       : angle       4.69083 /  3.28 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 287
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  961 ASP cc_start: 0.7602 (p0) cc_final: 0.7373 (p0)
REVERT: A 1034 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8666 (pt0)
REVERT: A 1081 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7686 (mpp)
REVERT: B  907 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8138 (pp)
REVERT: B  913 PHE cc_start: 0.7876 (t80) cc_final: 0.7250 (t80)
REVERT: B  916 GLN cc_start: 0.7570 (pm20) cc_final: 0.7330 (pm20)
REVERT: B 1081 MET cc_start: 0.8150 (tpp) cc_final: 0.7853 (tpp)
REVERT: C  965 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8056 (ttmm)
REVERT: C 1008 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: D  907 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8105 (pp)
REVERT: E 1043 ARG cc_start: 0.8755 (mtt90) cc_final: 0.8014 (mtt90)
REVERT: F  951 LYS cc_start: 0.9114 (tptm) cc_final: 0.8913 (tttp)
REVERT: G  907 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8200 (pp)
  outliers start: 69
  outliers final: 50
  residues processed: 325
  average time/residue: 0.1190
  time to fit residues: 51.6338
Evaluate side-chains
  328 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 273
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1070 HIS
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue 1003 SER
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  963 ASP
Chi-restraints excluded: chain C residue 1003 SER
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  915 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue  989 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain D residue 1058 GLU
Chi-restraints excluded: chain E residue  915 LEU
Chi-restraints excluded: chain E residue  919 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1017 CYS
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1017 CYS
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue  963 ASP
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C1070 HIS
D 953 ASN
D1070 HIS
E 953 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.069868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.059273 restraints weight = 31052.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.98
r_work: 0.2797 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10479  Z= 0.172
  Angle     :  0.738  12.687  14266  Z= 0.374
  Chirality :  0.051   0.148   1687
  Planarity :  0.005   0.041   1827
  Dihedral  :  5.149  28.352   1387
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 28.30 %
    Favored  : 64.83 %
  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: -0.04 (0.24), residues: 1295
  helix:  2.16 (0.25), residues: 441
  sheet:  1.53 (0.33), residues: 224
  loop : -2.42 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B1043 
 TYR   0.005   0.001   TYR E1045 
 PHE   0.014   0.002   PHE C 919 
 TRP   0.014   0.001   TRP G 962 
 HIS   0.023   0.002   HIS C1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.17 (10479)
  covalent geometry    : angle       0.73818 /  0.37 (14266)
  hydrogen bonds       : bond        0.04494 /  2.99 (  516)
  hydrogen bonds       : angle       4.68414 /  3.27 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 277
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  982 TRP cc_start: 0.8601 (m100) cc_final: 0.8382 (m100)
REVERT: A 1034 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8671 (pm20)
REVERT: A 1081 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7559 (mpp)
REVERT: B  907 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8202 (pp)
REVERT: B  913 PHE cc_start: 0.7903 (t80) cc_final: 0.7281 (t80)
REVERT: B 1043 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8447 (mtt90)
REVERT: B 1081 MET cc_start: 0.8431 (tpp) cc_final: 0.8049 (tpp)
REVERT: C  965 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8212 (ttmm)
REVERT: C  995 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8638 (mm)
REVERT: D  907 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8167 (pp)
REVERT: D 1043 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8229 (mtm-85)
REVERT: E 1043 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8124 (mtt90)
REVERT: G  907 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8278 (pp)
REVERT: G 1043 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8275 (mtm-85)
  outliers start: 76
  outliers final: 57
  residues processed: 322
  average time/residue: 0.1194
  time to fit residues: 51.0868
Evaluate side-chains
  338 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 275
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1012 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue 1003 SER
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1058 GLU
Chi-restraints excluded: chain B residue 1070 HIS
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  963 ASP
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1003 SER
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue  989 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain E residue  919 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain E residue 1070 HIS
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1058 GLU
Chi-restraints excluded: chain F residue 1070 HIS
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  915 LEU
Chi-restraints excluded: chain G residue  934 ILE
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1058 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 113 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 90 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1070 HIS
C1070 HIS
D1070 HIS
E 953 ASN
E1051 HIS
E1061 GLN
E1070 HIS
F1070 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.069980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.059221 restraints weight = 31122.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.99
r_work: 0.2791 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10479  Z= 0.165
  Angle     :  0.750  10.323  14266  Z= 0.379
  Chirality :  0.051   0.146   1687
  Planarity :  0.006   0.045   1827
  Dihedral  :  5.209  25.495   1387
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 28.03 %
    Favored  : 64.74 %
  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: -0.12 (0.24), residues: 1295
  helix:  1.94 (0.25), residues: 448
  sheet:  1.49 (0.31), residues: 238
  loop : -2.49 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1052 
 TYR   0.004   0.001   TYR D1045 
 PHE   0.019   0.002   PHE D1079 
 TRP   0.017   0.001   TRP F 962 
 HIS   0.003   0.001   HIS C1057 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.16 (10479)
  covalent geometry    : angle       0.75002 /  0.38 (14266)
  hydrogen bonds       : bond        0.04382 /  2.92 (  516)
  hydrogen bonds       : angle       4.67099 /  3.27 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 280
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A 1034 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8645 (pm20)
REVERT: A 1081 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7577 (mpp)
REVERT: B  907 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8245 (pp)
REVERT: B 1043 ARG cc_start: 0.8698 (mtt90) cc_final: 0.8379 (mtt90)
REVERT: B 1081 MET cc_start: 0.8369 (tpp) cc_final: 0.7979 (tpp)
REVERT: C  913 PHE cc_start: 0.8077 (t80) cc_final: 0.7818 (t80)
REVERT: C  995 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8613 (mm)
REVERT: D  907 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8194 (pp)
REVERT: F 1004 GLU cc_start: 0.8801 (pm20) cc_final: 0.8549 (pm20)
REVERT: G  907 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (pp)
  outliers start: 80
  outliers final: 63
  residues processed: 328
  average time/residue: 0.1215
  time to fit residues: 53.1781
Evaluate side-chains
  336 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 267
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1012 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue 1003 SER
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1058 GLU
Chi-restraints excluded: chain B residue 1070 HIS
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  963 ASP
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1003 SER
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  915 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue  989 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1049 MET
Chi-restraints excluded: chain D residue 1070 HIS
Chi-restraints excluded: chain E residue  919 PHE
Chi-restraints excluded: chain E residue  930 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain E residue 1058 GLU
Chi-restraints excluded: chain E residue 1070 HIS
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1012 THR
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1058 GLU
Chi-restraints excluded: chain F residue 1070 HIS
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue  963 ASP
Chi-restraints excluded: chain G residue  976 THR
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1058 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 69 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0040
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0000
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.3596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1070 HIS
B1070 HIS
C1070 HIS
D1070 HIS
E 953 ASN
E1070 HIS
F1070 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.060452 restraints weight = 30734.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 3.01
r_work: 0.2824 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10479  Z= 0.141
  Angle     :  0.751  11.944  14266  Z= 0.377
  Chirality :  0.050   0.157   1687
  Planarity :  0.005   0.044   1827
  Dihedral  :  5.048  26.598   1387
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 29.39 %
    Favored  : 63.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.01 (0.24), residues: 1295
  helix:  2.07 (0.25), residues: 448
  sheet:  1.57 (0.31), residues: 238
  loop : -2.46 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1052 
 TYR   0.003   0.001   TYR G1045 
 PHE   0.013   0.001   PHE D 919 
 TRP   0.018   0.001   TRP F 962 
 HIS   0.012   0.001   HIS E1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 (10479)
  covalent geometry    : angle       0.75146 /  0.38 (14266)
  hydrogen bonds       : bond        0.03860 /  2.56 (  516)
  hydrogen bonds       : angle       4.53544 /  3.17 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 277
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  903 LEU cc_start: 0.8494 (mm) cc_final: 0.8114 (pp)
REVERT: A 1081 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7502 (mpp)
REVERT: B  907 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8234 (pp)
REVERT: B  916 GLN cc_start: 0.7719 (pm20) cc_final: 0.7098 (pm20)
REVERT: B  917 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8025 (mm-30)
REVERT: B 1043 ARG cc_start: 0.8676 (mtt90) cc_final: 0.8381 (mtt90)
REVERT: B 1081 MET cc_start: 0.8294 (tpp) cc_final: 0.7990 (tpp)
REVERT: C  913 PHE cc_start: 0.8024 (t80) cc_final: 0.7793 (t80)
REVERT: C  953 ASN cc_start: 0.8851 (t0) cc_final: 0.8565 (m-40)
REVERT: C  977 GLU cc_start: 0.7972 (mp0) cc_final: 0.7635 (mp0)
REVERT: C  995 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8616 (mm)
REVERT: C 1004 GLU cc_start: 0.8585 (pm20) cc_final: 0.8356 (pm20)
REVERT: C 1008 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8611 (tm-30)
REVERT: D  907 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (pp)
REVERT: D 1043 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8215 (mtt90)
REVERT: F  965 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8566 (ttmm)
REVERT: G  907 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8365 (pp)
REVERT: G 1043 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8258 (mtm-85)
  outliers start: 74
  outliers final: 58
  residues processed: 316
  average time/residue: 0.1192
  time to fit residues: 50.2088
Evaluate side-chains
  335 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 272
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  930 PHE
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  919 PHE
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1058 GLU
Chi-restraints excluded: chain B residue 1070 HIS
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  959 ILE
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  919 PHE
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain D residue 1049 MET
Chi-restraints excluded: chain D residue 1070 HIS
Chi-restraints excluded: chain E residue  930 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1019 LEU
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain E residue 1058 GLU
Chi-restraints excluded: chain E residue 1070 HIS
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1070 HIS
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  913 PHE
Chi-restraints excluded: chain G residue  919 PHE
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue  963 ASP
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 115 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1070 HIS
B1070 HIS
C1070 HIS
E 953 ASN
E1061 GLN
E1070 HIS
F1070 HIS
G 981 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.070503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.059736 restraints weight = 30713.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 2.99
r_work: 0.2807 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10479  Z= 0.157
  Angle     :  0.773  12.245  14266  Z= 0.387
  Chirality :  0.050   0.158   1687
  Planarity :  0.006   0.045   1827
  Dihedral  :  5.139  26.322   1387
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 29.93 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.00 (0.24), residues: 1295
  helix:  2.07 (0.25), residues: 448
  sheet:  1.61 (0.32), residues: 238
  loop : -2.47 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D1016 
 TYR   0.004   0.001   TYR A1045 
 PHE   0.017   0.002   PHE D1029 
 TRP   0.014   0.001   TRP G 962 
 HIS   0.008   0.001   HIS B1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.16 (10479)
  covalent geometry    : angle       0.77252 /  0.39 (14266)
  hydrogen bonds       : bond        0.04043 /  2.68 (  516)
  hydrogen bonds       : angle       4.54279 /  3.17 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 271
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  903 LEU cc_start: 0.8502 (mm) cc_final: 0.8119 (pp)
REVERT: A 1034 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8613 (pm20)
REVERT: A 1081 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7552 (mpp)
REVERT: B  907 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8296 (pp)
REVERT: B  916 GLN cc_start: 0.7774 (pm20) cc_final: 0.7482 (pm20)
REVERT: B  917 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8243 (mm-30)
REVERT: B 1043 ARG cc_start: 0.8679 (mtt90) cc_final: 0.8354 (mtt90)
REVERT: B 1081 MET cc_start: 0.8400 (tpp) cc_final: 0.7967 (tpp)
REVERT: C  953 ASN cc_start: 0.8854 (t0) cc_final: 0.8579 (m-40)
REVERT: C  977 GLU cc_start: 0.7930 (mp0) cc_final: 0.7638 (mp0)
REVERT: C  995 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8633 (mm)
REVERT: D  907 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8215 (pp)
REVERT: D  916 GLN cc_start: 0.7901 (pm20) cc_final: 0.7624 (pm20)
REVERT: D 1043 ARG cc_start: 0.8784 (mtt90) cc_final: 0.8269 (mtt90)
REVERT: E  982 TRP cc_start: 0.8615 (m100) cc_final: 0.8411 (m100)
REVERT: F  965 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8567 (ttmm)
REVERT: F 1004 GLU cc_start: 0.8771 (pm20) cc_final: 0.8568 (pm20)
REVERT: G  907 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8406 (pp)
REVERT: G 1016 ARG cc_start: 0.7414 (tmm160) cc_final: 0.7182 (tmm160)
REVERT: G 1043 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8240 (mtm-85)
  outliers start: 73
  outliers final: 60
  residues processed: 311
  average time/residue: 0.1109
  time to fit residues: 46.8064
Evaluate side-chains
  322 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 256
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1058 GLU
Chi-restraints excluded: chain B residue 1070 HIS
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  959 ILE
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1049 MET
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain D residue 1049 MET
Chi-restraints excluded: chain E residue  919 PHE
Chi-restraints excluded: chain E residue  930 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1019 LEU
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain F residue  919 PHE
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1012 THR
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1058 GLU
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  913 PHE
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue  963 ASP
Chi-restraints excluded: chain G residue  976 THR
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 64 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 122 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1070 HIS
B1070 HIS
C1070 HIS
D1070 HIS
E 953 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.070134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.059406 restraints weight = 30641.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.98
r_work: 0.2800 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10479  Z= 0.162
  Angle     :  0.791  12.349  14266  Z= 0.398
  Chirality :  0.050   0.158   1687
  Planarity :  0.006   0.043   1827
  Dihedral  :  5.198  26.500   1387
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 30.20 %
    Favored  : 63.11 %
  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: -0.02 (0.24), residues: 1295
  helix:  2.04 (0.25), residues: 448
  sheet:  1.61 (0.32), residues: 238
  loop : -2.49 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1052 
 TYR   0.004   0.001   TYR D1045 
 PHE   0.015   0.002   PHE D1029 
 TRP   0.016   0.001   TRP G 962 
 HIS   0.007   0.001   HIS C1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.16 (10479)
  covalent geometry    : angle       0.79147 /  0.40 (14266)
  hydrogen bonds       : bond        0.04086 /  2.72 (  516)
  hydrogen bonds       : angle       4.55456 /  3.17 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 256
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  903 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8085 (pp)
REVERT: A 1034 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8621 (pm20)
REVERT: A 1081 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7557 (mpp)
REVERT: B  907 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8327 (pp)
REVERT: B 1043 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8351 (mtt90)
REVERT: B 1081 MET cc_start: 0.8400 (tpp) cc_final: 0.7945 (tpp)
REVERT: C  953 ASN cc_start: 0.8858 (t0) cc_final: 0.8593 (m-40)
REVERT: C  977 GLU cc_start: 0.7937 (mp0) cc_final: 0.7645 (mp0)
REVERT: C  995 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8639 (mm)
REVERT: D  907 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8222 (pp)
REVERT: D  916 GLN cc_start: 0.7911 (pm20) cc_final: 0.7658 (pm20)
REVERT: D  977 GLU cc_start: 0.7843 (mp0) cc_final: 0.7618 (mp0)
REVERT: E 1048 GLU cc_start: 0.7314 (pm20) cc_final: 0.6956 (pp20)
REVERT: F  965 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8602 (ttmm)
REVERT: F 1004 GLU cc_start: 0.8805 (pm20) cc_final: 0.8588 (pm20)
REVERT: G  907 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8427 (pp)
REVERT: G 1016 ARG cc_start: 0.7429 (tmm160) cc_final: 0.7191 (tmm160)
  outliers start: 74
  outliers final: 59
  residues processed: 297
  average time/residue: 0.1083
  time to fit residues: 43.4357
Evaluate side-chains
  319 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 253
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1034 GLN
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain B residue 1058 GLU
Chi-restraints excluded: chain C residue  903 LEU
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  959 ILE
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  915 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain D residue 1049 MET
Chi-restraints excluded: chain E residue  930 PHE
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1019 LEU
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain E residue 1070 HIS
Chi-restraints excluded: chain F residue  919 PHE
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1012 THR
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1058 GLU
Chi-restraints excluded: chain F residue 1070 HIS
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  913 PHE
Chi-restraints excluded: chain G residue  949 VAL
Chi-restraints excluded: chain G residue  976 THR
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 116 optimal weight:    0.4980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C1070 HIS
E 953 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.058696 restraints weight = 30505.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 2.94
r_work: 0.2781 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10479  Z= 0.182
  Angle     :  0.825  12.239  14266  Z= 0.417
  Chirality :  0.051   0.156   1687
  Planarity :  0.006   0.050   1827
  Dihedral  :  5.388  28.074   1387
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 31.56 %
    Favored  : 62.39 %
  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: -0.11 (0.24), residues: 1295
  helix:  1.92 (0.25), residues: 448
  sheet:  1.57 (0.32), residues: 238
  loop : -2.50 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D1016 
 TYR   0.005   0.001   TYR D1045 
 PHE   0.017   0.002   PHE A 919 
 TRP   0.016   0.001   TRP G 962 
 HIS   0.003   0.001   HIS A1057 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.18 (10479)
  covalent geometry    : angle       0.82499 /  0.42 (14266)
  hydrogen bonds       : bond        0.04374 /  2.91 (  516)
  hydrogen bonds       : angle       4.62483 /  3.21 ( 1467)

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

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

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2590 Ramachandran restraints generated.
    1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 257
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1081 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7600 (mpp)
REVERT: B  907 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8404 (pp)
REVERT: B 1043 ARG cc_start: 0.8685 (mtt90) cc_final: 0.8366 (mtt90)
REVERT: B 1081 MET cc_start: 0.8464 (tpp) cc_final: 0.8004 (tpp)
REVERT: C  953 ASN cc_start: 0.8881 (t0) cc_final: 0.8643 (m-40)
REVERT: C  995 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8644 (mm)
REVERT: D  907 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8255 (pp)
REVERT: D  977 GLU cc_start: 0.7770 (mp0) cc_final: 0.7566 (mp0)
REVERT: D 1043 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8167 (mtt90)
REVERT: E 1048 GLU cc_start: 0.7381 (pm20) cc_final: 0.7009 (pp20)
REVERT: F  965 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8592 (ttmm)
REVERT: F 1004 GLU cc_start: 0.8792 (pm20) cc_final: 0.8577 (pm20)
REVERT: G  907 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (pp)
  outliers start: 67
  outliers final: 54
  residues processed: 298
  average time/residue: 0.1106
  time to fit residues: 44.6667
Evaluate side-chains
  313 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 253
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue  960 SER
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1070 HIS
Chi-restraints excluded: chain A residue 1081 MET
Chi-restraints excluded: chain B residue  907 LEU
Chi-restraints excluded: chain B residue  949 VAL
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain B residue 1019 LEU
Chi-restraints excluded: chain B residue 1027 GLU
Chi-restraints excluded: chain C residue  903 LEU
Chi-restraints excluded: chain C residue  907 LEU
Chi-restraints excluded: chain C residue  935 ARG
Chi-restraints excluded: chain C residue  948 SER
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  976 THR
Chi-restraints excluded: chain C residue  995 ILE
Chi-restraints excluded: chain C residue 1019 LEU
Chi-restraints excluded: chain C residue 1027 GLU
Chi-restraints excluded: chain C residue 1070 HIS
Chi-restraints excluded: chain D residue  907 LEU
Chi-restraints excluded: chain D residue  915 LEU
Chi-restraints excluded: chain D residue  976 THR
Chi-restraints excluded: chain D residue 1003 SER
Chi-restraints excluded: chain D residue 1019 LEU
Chi-restraints excluded: chain D residue 1049 MET
Chi-restraints excluded: chain E residue  949 VAL
Chi-restraints excluded: chain E residue  958 THR
Chi-restraints excluded: chain E residue  960 SER
Chi-restraints excluded: chain E residue  976 THR
Chi-restraints excluded: chain E residue 1003 SER
Chi-restraints excluded: chain E residue 1019 LEU
Chi-restraints excluded: chain E residue 1049 MET
Chi-restraints excluded: chain F residue  935 ARG
Chi-restraints excluded: chain F residue  949 VAL
Chi-restraints excluded: chain F residue  958 THR
Chi-restraints excluded: chain F residue  960 SER
Chi-restraints excluded: chain F residue  965 LYS
Chi-restraints excluded: chain F residue  976 THR
Chi-restraints excluded: chain F residue 1003 SER
Chi-restraints excluded: chain F residue 1012 THR
Chi-restraints excluded: chain F residue 1019 LEU
Chi-restraints excluded: chain F residue 1039 ILE
Chi-restraints excluded: chain F residue 1058 GLU
Chi-restraints excluded: chain G residue  907 LEU
Chi-restraints excluded: chain G residue  976 THR
Chi-restraints excluded: chain G residue  989 THR
Chi-restraints excluded: chain G residue 1003 SER
Chi-restraints excluded: chain G residue 1019 LEU
Chi-restraints excluded: chain G residue 1027 GLU
Chi-restraints excluded: chain G residue 1070 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 118 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 121 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1070 HIS
C1070 HIS
E 953 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.069466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.058867 restraints weight = 30832.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.98
r_work: 0.2786 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10479  Z= 0.172
  Angle     :  0.832  12.127  14266  Z= 0.418
  Chirality :  0.051   0.165   1687
  Planarity :  0.006   0.043   1827
  Dihedral  :  5.372  30.225   1387
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 31.74 %
    Favored  : 62.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.13 (0.24), residues: 1295
  helix:  1.88 (0.25), residues: 448
  sheet:  1.60 (0.32), residues: 238
  loop : -2.51 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 990 
 TYR   0.003   0.001   TYR D1045 
 PHE   0.015   0.002   PHE D 919 
 TRP   0.016   0.001   TRP G 962 
 HIS   0.005   0.001   HIS C1070 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.17 (10479)
  covalent geometry    : angle       0.83178 /  0.42 (14266)
  hydrogen bonds       : bond        0.04262 /  2.84 (  516)
  hydrogen bonds       : angle       4.61949 /  3.21 ( 1467)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2179.12 seconds
wall clock time: 38 minutes 8.85 seconds (2288.85 seconds total)