Starting phenix.real_space_refine
on Sat Dec 28 21:00:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/12_2024/8dk3_27482.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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: 6
    Type Number    sf(0)   Gaussians
     P      58      5.49       5
     Mg      2      5.21       5
     S      23      5.16       5
     C    5414      2.51       5
     N    1597      2.21       5
     O    1811      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8905
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3530
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 12, 'TRANS': 442}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3494
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 12, 'TRANS': 437}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 751
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
    Chain: "P"
      Number of atoms: 520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 520
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "Q"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 546
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.69, per 1000 atoms: 0.64
  Number of scatterers: 8905
  At special positions: 0
  Unit cell: (89.1, 111.1, 112.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      23     16.00
     P      58     15.00
     Mg      2     11.99
     O    1811      8.00
     N    1597      7.00
     C    5414      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: 2.22
  Conformation dependent library (CDL) restraints added in 960.9 milliseconds
  

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      46.0% alpha, 18.5% beta
      26 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 2.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 59
      removed outlier: 3.770A  pdb=" N   LEU A  52 " --> pdb=" O   GLY A  48 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   LEU A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 72
      removed outlier: 3.536A  pdb=" N   THR A  71 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 86
      removed outlier: 3.528A  pdb=" N   TYR A  83 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 162
      removed outlier: 3.609A  pdb=" N   ALA A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 175
      removed outlier: 3.883A  pdb=" N   MET A 171 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLU A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASP A 174 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
    Processing helix  chain 'A' and resid 200 through 208
    Processing helix  chain 'A' and resid 216 through 224
      removed outlier: 3.926A  pdb=" N   ILE A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 857 through 881
    Processing helix  chain 'A' and resid 902 through 915
      removed outlier: 4.495A  pdb=" N   THR A 906 " --> pdb=" O   GLU A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 944
      removed outlier: 3.841A  pdb=" N   VAL A 935 " --> pdb=" O   LEU A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 955
    Processing helix  chain 'A' and resid 956 through 958
      No H-bonds generated for 'chain 'A' and resid 956 through 958'
    Processing helix  chain 'A' and resid 985 through 1005
      removed outlier: 3.719A  pdb=" N   LYS A 989 " --> pdb=" O   SER A 985 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLU A 990 " --> pdb=" O   GLY A 986 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 991 " --> pdb=" O   GLY A 987 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1010
    Processing helix  chain 'A' and resid 1028 through 1043
      removed outlier: 3.649A  pdb=" N   ALA A1032 " --> pdb=" O   SER A1028 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY A1033 " --> pdb=" O   HIS A1029 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A1034 " --> pdb=" O   ALA A1030 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A1043 " --> pdb=" O   LEU A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1062
      removed outlier: 3.684A  pdb=" N   ARG A1059 " --> pdb=" O   MET A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1088
      removed outlier: 3.645A  pdb=" N   HIS A1088 " --> pdb=" O   ALA A1084 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 59
      removed outlier: 3.557A  pdb=" N   LEU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 72
      removed outlier: 3.655A  pdb=" N   THR B  71 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 3.648A  pdb=" N   TYR B  83 " --> pdb=" O   ASP B  79 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG B  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
      removed outlier: 3.875A  pdb=" N   LEU B 139 " --> pdb=" O   ALA B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 163
    Processing helix  chain 'B' and resid 164 through 170
    Processing helix  chain 'B' and resid 183 through 196
    Processing helix  chain 'B' and resid 200 through 208
    Processing helix  chain 'B' and resid 216 through 224
      removed outlier: 3.768A  pdb=" N   ILE B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 241
    Processing helix  chain 'B' and resid 858 through 882
      removed outlier: 3.733A  pdb=" N   ILE B 870 " --> pdb=" O   GLU B 866 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU B 871 " --> pdb=" O   VAL B 867 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP B 876 " --> pdb=" O   GLU B 872 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 901 through 918
      removed outlier: 3.986A  pdb=" N   ARG B 905 " --> pdb=" O   HIS B 901 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG B 918 " --> pdb=" O   LEU B 914 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 930 through 944
      removed outlier: 4.384A  pdb=" N   LEU B 934 " --> pdb=" O   ALA B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 947 through 955
      removed outlier: 4.047A  pdb=" N   LEU B 953 " --> pdb=" O   GLY B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 956 through 958
      No H-bonds generated for 'chain 'B' and resid 956 through 958'
    Processing helix  chain 'B' and resid 985 through 1005
      removed outlier: 3.760A  pdb=" N   LYS B 989 " --> pdb=" O   SER B 985 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   GLU B 990 " --> pdb=" O   GLY B 986 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE B 991 " --> pdb=" O   GLY B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1028 through 1043
      removed outlier: 3.613A  pdb=" N   PHE B1042 " --> pdb=" O   ALA B1038 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY B1043 " --> pdb=" O   LEU B1039 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1054 through 1062
      removed outlier: 3.941A  pdb=" N   HIS B1060 " --> pdb=" O   ARG B1056 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   HIS B1061 " --> pdb=" O   LEU B1057 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 425
    Processing helix  chain 'C' and resid 429 through 437
    Processing helix  chain 'C' and resid 445 through 457
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33
      removed outlier: 6.875A  pdb=" N   GLY A  28 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU A  15 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   GLU A 115 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER A  17 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 111 " --> pdb=" O   GLU A  19 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA A 109 " --> pdb=" O   TYR A  21 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   TRP A  23 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 11.602A  pdb=" N   VAL A 107 " --> pdb=" O   TRP A  23 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 116 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS A 140 " --> pdb=" O   TRP A 128 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1018 through 1021
      removed outlier: 3.747A  pdb=" N   THR A  39 " --> pdb=" O   ALA A1046 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLU A1074 " --> pdb=" O   ARG A1071 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 898
      removed outlier: 4.160A  pdb=" N   GLU A 976 " --> pdb=" O   VAL A 966 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ASP A 968 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU A 974 " --> pdb=" O   ASP A 968 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33
      removed outlier: 6.164A  pdb=" N   GLY B  28 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   TYR B  21 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   HIS B  30 " --> pdb=" O   GLU B  19 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   GLU B  19 " --> pdb=" O   HIS B  30 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ALA B  32 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   SER B  17 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   THR B 113 " --> pdb=" O   THR B  16 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ILE B  18 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ALA B 111 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LEU B  20 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ALA B 109 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   ASN B  22 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL B 107 " --> pdb=" O   ASN B  22 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA B 125 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU B 144 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TRP B 128 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1017 through 1019
      removed outlier: 4.067A  pdb=" N   ALA B1065 " --> pdb=" O   LEU B1080 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 890 through 898
      removed outlier: 3.847A  pdb=" N   GLU B 976 " --> pdb=" O   VAL B 966 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ASP B 968 " --> pdb=" O   LEU B 974 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 974 " --> pdb=" O   ASP B 968 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 460 through 472
      removed outlier: 7.253A  pdb=" N   GLU C 464 " --> pdb=" O   TYR C 484 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR C 484 " --> pdb=" O   GLU C 464 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ASP C 472 " --> pdb=" O   GLN C 476 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   GLN C 476 " --> pdb=" O   ASP C 472 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.36: 2961
        1.36 -     1.50: 2895
        1.50 -     1.65: 3283
        1.65 -     1.80: 22
        1.80 -     1.94: 16
  Bond restraints: 9177
  Sorted by residual:
  bond pdb=" N   ASN B  63 "
       pdb=" CA  ASN B  63 "
    ideal  model  delta    sigma   weight residual
    1.464  1.454  0.010 9.80e-03 1.04e+04 9.60e-01
  bond pdb=" CB  VAL A 197 "
       pdb=" CG1 VAL A 197 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.73e-01
  bond pdb=" CB  VAL B1068 "
       pdb=" CG2 VAL B1068 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.55e-01
  bond pdb=" CB  THR B1062 "
       pdb=" CG2 THR B1062 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.54e-01
  bond pdb=" CA  THR B  88 "
       pdb=" CB  THR B  88 "
    ideal  model  delta    sigma   weight residual
    1.531  1.501  0.029 3.28e-02 9.30e+02 8.05e-01
  ... (remaining 9172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 12079
        1.26 -     2.52: 488
        2.52 -     3.78: 64
        3.78 -     5.04: 11
        5.04 -     6.30: 3
  Bond angle restraints: 12645
  Sorted by residual:
  angle pdb=" C   GLU C 475 "
        pdb=" CA  GLU C 475 "
        pdb=" CB  GLU C 475 "
      ideal   model   delta    sigma   weight residual
     116.54  110.24    6.30 1.15e+00 7.56e-01 3.00e+01
  angle pdb=" CA  GLU C 475 "
        pdb=" C   GLU C 475 "
        pdb=" N   GLN C 476 "
      ideal   model   delta    sigma   weight residual
     119.52  116.45    3.07 7.90e-01 1.60e+00 1.51e+01
  angle pdb=" N   GLY B1016 "
        pdb=" CA  GLY B1016 "
        pdb=" C   GLY B1016 "
      ideal   model   delta    sigma   weight residual
     113.18  118.20   -5.02 2.37e+00 1.78e-01 4.49e+00
  angle pdb=" N   GLU C 475 "
        pdb=" CA  GLU C 475 "
        pdb=" C   GLU C 475 "
      ideal   model   delta    sigma   weight residual
     108.31  111.46   -3.15 1.52e+00 4.33e-01 4.28e+00
  angle pdb=" C   ALA B  62 "
        pdb=" N   ASN B  63 "
        pdb=" CA  ASN B  63 "
      ideal   model   delta    sigma   weight residual
     122.28  120.54    1.74 8.80e-01 1.29e+00 3.93e+00
  ... (remaining 12640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.79: 4886
       22.79 -    45.58: 366
       45.58 -    68.38: 135
       68.38 -    91.17: 1
       91.17 -   113.96: 1
  Dihedral angle restraints: 5389
    sinusoidal: 2542
      harmonic: 2847
  Sorted by residual:
  dihedral pdb=" O1A AGS A1201 "
           pdb=" O3A AGS A1201 "
           pdb=" PA  AGS A1201 "
           pdb=" PB  AGS A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   46.23 -113.96     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" CA  GLN A 887 "
           pdb=" C   GLN A 887 "
           pdb=" N   PRO A 888 "
           pdb=" CA  PRO A 888 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.70  -16.30     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  ARG B  78 "
           pdb=" CG  ARG B  78 "
           pdb=" CD  ARG B  78 "
           pdb=" NE  ARG B  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.84   58.84     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 5386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 744
       0.026 -    0.053: 441
       0.053 -    0.079: 143
       0.079 -    0.105: 62
       0.105 -    0.132: 30
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  ILE B 110 "
            pdb=" N   ILE B 110 "
            pdb=" C   ILE B 110 "
            pdb=" CB  ILE B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  PRO B 888 "
            pdb=" N   PRO B 888 "
            pdb=" C   PRO B 888 "
            pdb=" CB  PRO B 888 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" PA  AGS A1201 "
            pdb=" O2A AGS A1201 "
            pdb=" O3A AGS A1201 "
            pdb=" O5' AGS A1201 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       3.18    3.05    0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1417 not shown)

  Planarity restraints: 1447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 887 "    0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO B 888 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 888 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 888 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 179 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO B 180 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 180 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 180 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  35 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO B  36 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B  36 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  36 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1444 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 40
        2.48 -     3.08: 5910
        3.08 -     3.69: 12225
        3.69 -     4.29: 17153
        4.29 -     4.90: 28481
  Nonbonded interactions: 63809
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  50 "
            pdb="MG    MG B1202 "
     model   vdw
     1.869 2.170
  nonbonded pdb=" O2B AGS A1201 "
            pdb="MG    MG A1202 "
     model   vdw
     1.929 2.170
  nonbonded pdb=" OG1 THR A  50 "
            pdb="MG    MG A1202 "
     model   vdw
     1.982 2.170
  nonbonded pdb=" O2B AGS A1201 "
            pdb=" O2G AGS A1201 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER C 429 "
            pdb=" OE1 GLU C 432 "
     model   vdw
     2.159 3.040
  ... (remaining 63804 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 10 through 242 or resid 857 through 1083 or resid 1201 thr \ 
ough 1202))
  selection = (chain 'B' and (resid 10 through 917 or resid 929 through 1083 or resid 1201 thr \ 
ough 1202))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  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:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.100
  Process input model:                     25.050
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   9177  Z= 0.380
  Angle     :  0.579   6.299  12645  Z= 0.320
  Chirality :  0.040   0.132   1420
  Planarity :  0.004   0.046   1447
  Dihedral  : 16.396 113.958   3555
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  6.33 %
    Favored  : 92.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.28), residues: 985
  helix:  1.71 (0.27), residues: 394
  sheet: -0.59 (0.36), residues: 204
  loop : -1.73 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 128 
 HIS   0.005   0.001   HIS B1045 
 PHE   0.013   0.001   PHE B 187 
 TYR   0.012   0.001   TYR B 862 
 ARG   0.003   0.000   ARG B1059 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8663 (p-80) cc_final: 0.8447 (p-80)
REVERT: C  409 ASP cc_start: 0.8641 (t0) cc_final: 0.8061 (t0)
REVERT: C  476 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8688 (mm110)
REVERT: C  495 ILE cc_start: 0.9033 (tp) cc_final: 0.8742 (pt)
  outliers start: 7
  outliers final: 3
  residues processed: 49
  average time/residue: 0.2493
  time to fit residues: 17.3096
Evaluate side-chains
  36 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue 1018 ILE
Chi-restraints excluded: chain B residue 1019 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0060
   chunk 41 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
A 103 GLN
A1022 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9177  Z= 0.155
  Angle     :  0.542   6.548  12645  Z= 0.297
  Chirality :  0.038   0.159   1420
  Planarity :  0.004   0.042   1447
  Dihedral  : 18.950 114.817   1751
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.15 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.27), residues: 985
  helix:  1.74 (0.27), residues: 402
  sheet: -0.27 (0.36), residues: 205
  loop : -1.72 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 901 
 PHE   0.007   0.001   PHE C 467 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.007   0.000   ARG A 883 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8624 (p-80) cc_final: 0.8408 (p-80)
REVERT: C  409 ASP cc_start: 0.8449 (t0) cc_final: 0.7720 (t0)
REVERT: C  495 ILE cc_start: 0.8982 (tp) cc_final: 0.8691 (pt)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.1873
  time to fit residues: 13.6205
Evaluate side-chains
  38 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0000
   chunk 101 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
A 944 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9177  Z= 0.213
  Angle     :  0.520   5.718  12645  Z= 0.288
  Chirality :  0.038   0.140   1420
  Planarity :  0.004   0.046   1447
  Dihedral  : 18.904 111.123   1748
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.61 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 985
  helix:  1.77 (0.27), residues: 402
  sheet: -0.21 (0.35), residues: 205
  loop : -1.78 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B1045 
 PHE   0.008   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.003   0.000   ARG A 883 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8612 (p-80) cc_final: 0.8402 (p-80)
REVERT: C  409 ASP cc_start: 0.8488 (t0) cc_final: 0.7698 (t0)
REVERT: C  465 ARG cc_start: 0.8358 (mmt180) cc_final: 0.7770 (mmt180)
REVERT: C  495 ILE cc_start: 0.8961 (tp) cc_final: 0.8716 (pt)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 0.2027
  time to fit residues: 14.0945
Evaluate side-chains
  41 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0040
   chunk 94 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.1996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9177  Z= 0.193
  Angle     :  0.509   6.919  12645  Z= 0.281
  Chirality :  0.037   0.140   1420
  Planarity :  0.003   0.042   1447
  Dihedral  : 18.891 106.074   1748
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.46 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.27), residues: 985
  helix:  1.82 (0.27), residues: 401
  sheet: -0.31 (0.35), residues: 208
  loop : -1.75 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.003   0.001   HIS C 415 
 PHE   0.007   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.001   0.000   ARG A  78 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8606 (p-80) cc_final: 0.8395 (p-80)
REVERT: B  974 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9091 (tt)
REVERT: C  409 ASP cc_start: 0.8511 (t0) cc_final: 0.7739 (t0)
REVERT: C  465 ARG cc_start: 0.8278 (mmt180) cc_final: 0.7672 (mmt180)
  outliers start: 10
  outliers final: 7
  residues processed: 47
  average time/residue: 0.1982
  time to fit residues: 14.0685
Evaluate side-chains
  44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9177  Z= 0.189
  Angle     :  0.499   5.979  12645  Z= 0.276
  Chirality :  0.037   0.140   1420
  Planarity :  0.003   0.045   1447
  Dihedral  : 18.933 103.373   1748
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.98 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.27), residues: 985
  helix:  1.91 (0.27), residues: 399
  sheet: -0.30 (0.35), residues: 208
  loop : -1.77 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.003   0.000   HIS B1045 
 PHE   0.007   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.001   0.000   ARG C 410 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8618 (p-80) cc_final: 0.8410 (p-80)
REVERT: B  974 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9114 (tt)
REVERT: C  409 ASP cc_start: 0.8530 (t0) cc_final: 0.7750 (t0)
REVERT: C  465 ARG cc_start: 0.8281 (mmt180) cc_final: 0.7688 (mmt180)
  outliers start: 16
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1966
  time to fit residues: 15.4674
Evaluate side-chains
  45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  880 THR
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   9177  Z= 0.445
  Angle     :  0.642   8.642  12645  Z= 0.346
  Chirality :  0.042   0.167   1420
  Planarity :  0.004   0.044   1447
  Dihedral  : 19.115 104.696   1748
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.44 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 985
  helix:  1.53 (0.27), residues: 400
  sheet: -0.51 (0.35), residues: 205
  loop : -1.98 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 128 
 HIS   0.007   0.001   HIS B1045 
 PHE   0.014   0.002   PHE B 187 
 TYR   0.015   0.002   TYR A 891 
 ARG   0.003   0.000   ARG A 169 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8606 (p-80) cc_final: 0.8394 (p-80)
REVERT: C  409 ASP cc_start: 0.8609 (t0) cc_final: 0.7837 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 42
  average time/residue: 0.1852
  time to fit residues: 12.3193
Evaluate side-chains
  42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  880 THR
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  495 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9177  Z= 0.160
  Angle     :  0.519   9.624  12645  Z= 0.284
  Chirality :  0.037   0.147   1420
  Planarity :  0.003   0.044   1447
  Dihedral  : 18.990  99.020   1748
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.56 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.27), residues: 985
  helix:  1.79 (0.27), residues: 399
  sheet: -0.46 (0.35), residues: 208
  loop : -1.82 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B1029 
 PHE   0.007   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.002   0.000   ARG A1040 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8572 (p-80) cc_final: 0.8351 (p-80)
REVERT: B  974 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9136 (tt)
REVERT: C  409 ASP cc_start: 0.8552 (t0) cc_final: 0.7780 (t0)
REVERT: C  465 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7708 (mmt180)
  outliers start: 12
  outliers final: 7
  residues processed: 46
  average time/residue: 0.1918
  time to fit residues: 13.4386
Evaluate side-chains
  42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  880 THR
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0370
   overall best weight:    1.1460

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9177  Z= 0.194
  Angle     :  0.514   8.036  12645  Z= 0.282
  Chirality :  0.037   0.140   1420
  Planarity :  0.003   0.045   1447
  Dihedral  : 19.039  98.115   1748
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.92 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.27), residues: 985
  helix:  1.89 (0.27), residues: 399
  sheet: -0.40 (0.35), residues: 208
  loop : -1.82 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.003   0.000   HIS B1045 
 PHE   0.006   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.001   0.000   ARG C 410 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8594 (p-80) cc_final: 0.8380 (p-80)
REVERT: B  974 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9128 (tt)
REVERT: C  409 ASP cc_start: 0.8494 (t0) cc_final: 0.7749 (t0)
REVERT: C  465 ARG cc_start: 0.8257 (mmt180) cc_final: 0.7654 (mmt180)
  outliers start: 12
  outliers final: 10
  residues processed: 46
  average time/residue: 0.2006
  time to fit residues: 14.0867
Evaluate side-chains
  45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  880 THR
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0060
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.9798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9177  Z= 0.172
  Angle     :  0.496   7.543  12645  Z= 0.273
  Chirality :  0.037   0.145   1420
  Planarity :  0.003   0.044   1447
  Dihedral  : 19.029  96.794   1748
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.92 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.27), residues: 985
  helix:  1.96 (0.27), residues: 399
  sheet: -0.35 (0.35), residues: 208
  loop : -1.76 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 128 
 HIS   0.002   0.000   HIS B1045 
 PHE   0.006   0.001   PHE A 221 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.002   0.000   ARG C 410 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8589 (p-80) cc_final: 0.8382 (p-80)
REVERT: B  974 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9140 (tt)
REVERT: C  409 ASP cc_start: 0.8481 (t0) cc_final: 0.7734 (t0)
REVERT: C  465 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7655 (mmt180)
  outliers start: 12
  outliers final: 10
  residues processed: 46
  average time/residue: 0.2075
  time to fit residues: 14.3336
Evaluate side-chains
  45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0870
   overall best weight:    0.6958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9177  Z= 0.147
  Angle     :  0.482   7.462  12645  Z= 0.266
  Chirality :  0.036   0.144   1420
  Planarity :  0.003   0.047   1447
  Dihedral  : 18.993  95.174   1748
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.80 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.27), residues: 985
  helix:  2.10 (0.27), residues: 399
  sheet: -0.29 (0.35), residues: 208
  loop : -1.75 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.002   0.000   HIS A 901 
 PHE   0.008   0.001   PHE C 467 
 TYR   0.014   0.001   TYR B 862 
 ARG   0.002   0.000   ARG C 426 

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  901 HIS cc_start: 0.8600 (p-80) cc_final: 0.8392 (p-80)
REVERT: B  974 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9134 (tt)
REVERT: C  409 ASP cc_start: 0.8482 (t0) cc_final: 0.7734 (t0)
REVERT: C  465 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7758 (mmt180)
  outliers start: 11
  outliers final: 8
  residues processed: 46
  average time/residue: 0.2148
  time to fit residues: 15.0296
Evaluate side-chains
  43 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  974 LEU
Chi-restraints excluded: chain B residue 1019 VAL
Chi-restraints excluded: chain B residue 1047 VAL
Chi-restraints excluded: chain B residue 1078 VAL
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.043966 restraints weight = 30853.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 3.37
r_work: 0.2612 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9177  Z= 0.309
  Angle     :  0.566  10.408  12645  Z= 0.306
  Chirality :  0.039   0.135   1420
  Planarity :  0.004   0.045   1447
  Dihedral  : 19.070  98.891   1748
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.41 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.27), residues: 985
  helix:  1.91 (0.27), residues: 399
  sheet: -0.43 (0.35), residues: 208
  loop : -1.83 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 128 
 HIS   0.005   0.001   HIS B1045 
 PHE   0.010   0.001   PHE B 187 
 TYR   0.013   0.001   TYR B 862 
 ARG   0.002   0.000   ARG A  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1617.75 seconds
wall clock time: 30 minutes 28.72 seconds (1828.72 seconds total)