Starting phenix.real_space_refine
on Sat Dec 28 06:57:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j87_36062/12_2024/8j87_36062.cif"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      22      5.16       5
     C    5058      2.51       5
     N    1346      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7846
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3923
          Classifications: {'peptide': 477}
          Link IDs: {'PTRANS': 22, 'TRANS': 454}
    Chain: "B"
      Number of atoms: 3923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3923
          Classifications: {'peptide': 477}
          Link IDs: {'PTRANS': 22, 'TRANS': 454}
  Time building chain proxies: 6.07, per 1000 atoms: 0.77
  Number of scatterers: 7846
  At special positions: 0
  Unit cell: (153.55, 72.21, 107.9, 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      22     16.00
     O    1420      8.00
     N    1346      7.00
     C    5058      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: 1.88
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 12 sheets defined
      49.4% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 716 through 729
      removed outlier: 3.519A  pdb=" N   LYS A 720 " --> pdb=" O   ARG A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 750
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 806 through 814
    Processing helix  chain 'A' and resid 818 through 822
      removed outlier: 3.518A  pdb=" N   LEU A 822 " --> pdb=" O   SER A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
      removed outlier: 3.841A  pdb=" N   MET A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 842 through 847'
    Processing helix  chain 'A' and resid 866 through 877
    Processing helix  chain 'A' and resid 883 through 893
      removed outlier: 3.847A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   HIS A 892 " --> pdb=" O   TYR A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 951
    Processing helix  chain 'A' and resid 954 through 960
      removed outlier: 4.009A  pdb=" N   THR A 958 " --> pdb=" O   SER A 954 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 959 " --> pdb=" O   ASN A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 984
      removed outlier: 3.992A  pdb=" N   LEU A 983 " --> pdb=" O   LYS A 979 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASN A 984 " --> pdb=" O   PRO A 980 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 979 through 984'
    Processing helix  chain 'A' and resid 985 through 989
      removed outlier: 3.839A  pdb=" N   GLU A 988 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU A 989 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 985 through 989'
    Processing helix  chain 'A' and resid 997 through 1003
      removed outlier: 3.963A  pdb=" N   LEU A1003 " --> pdb=" O   ILE A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.726A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
      removed outlier: 3.708A  pdb=" N   LEU A1056 " --> pdb=" O   ALA A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1092
      removed outlier: 4.027A  pdb=" N   ARG A1087 " --> pdb=" O   LYS A1083 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.715A  pdb=" N   ASN A1114 " --> pdb=" O   ILE A1110 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A1115 " --> pdb=" O   GLU A1111 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS A1116 " --> pdb=" O   GLU A1112 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN A1119 " --> pdb=" O   GLN A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.913A  pdb=" N   LEU A1133 " --> pdb=" O   ALA A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1158
      removed outlier: 3.874A  pdb=" N   LYS A1146 " --> pdb=" O   VAL A1142 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS A1147 " --> pdb=" O   GLU A1143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1187
      removed outlier: 3.524A  pdb=" N   TRP A1170 " --> pdb=" O   GLY A1166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 729
    Processing helix  chain 'B' and resid 738 through 750
    Processing helix  chain 'B' and resid 754 through 767
    Processing helix  chain 'B' and resid 806 through 814
    Processing helix  chain 'B' and resid 818 through 822
      removed outlier: 3.519A  pdb=" N   LEU B 822 " --> pdb=" O   SER B 819 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 847
      removed outlier: 3.840A  pdb=" N   MET B 846 " --> pdb=" O   PRO B 842 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 842 through 847'
    Processing helix  chain 'B' and resid 866 through 877
    Processing helix  chain 'B' and resid 883 through 893
      removed outlier: 3.847A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   HIS B 892 " --> pdb=" O   TYR B 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 951
    Processing helix  chain 'B' and resid 954 through 960
      removed outlier: 4.008A  pdb=" N   THR B 958 " --> pdb=" O   SER B 954 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 959 " --> pdb=" O   ASN B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 979 through 984
      removed outlier: 3.992A  pdb=" N   LEU B 983 " --> pdb=" O   LYS B 979 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASN B 984 " --> pdb=" O   PRO B 980 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 979 through 984'
    Processing helix  chain 'B' and resid 985 through 989
      removed outlier: 3.839A  pdb=" N   GLU B 988 " --> pdb=" O   ARG B 985 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU B 989 " --> pdb=" O   ILE B 986 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 985 through 989'
    Processing helix  chain 'B' and resid 997 through 1003
      removed outlier: 3.963A  pdb=" N   LEU B1003 " --> pdb=" O   ILE B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.726A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
      removed outlier: 3.706A  pdb=" N   LEU B1056 " --> pdb=" O   ALA B1052 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1083 through 1092
      removed outlier: 4.028A  pdb=" N   ARG B1087 " --> pdb=" O   LYS B1083 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE B1088 " --> pdb=" O   GLU B1084 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1119
      removed outlier: 3.716A  pdb=" N   ASN B1114 " --> pdb=" O   ILE B1110 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN B1115 " --> pdb=" O   GLU B1111 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS B1116 " --> pdb=" O   GLU B1112 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN B1119 " --> pdb=" O   GLN B1115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1133
      removed outlier: 3.914A  pdb=" N   LEU B1133 " --> pdb=" O   ALA B1130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1134 through 1158
      removed outlier: 3.875A  pdb=" N   LYS B1146 " --> pdb=" O   VAL B1142 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS B1147 " --> pdb=" O   GLU B1143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
      removed outlier: 3.524A  pdb=" N   TRP B1170 " --> pdb=" O   GLY B1166 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 736 through 737
      removed outlier: 3.615A  pdb=" N   GLN A 804 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.894A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913
      removed outlier: 3.519A  pdb=" N   SER A 919 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 926
      removed outlier: 6.146A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE A 931 " --> pdb=" O   SER A 926 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A 974 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS A 977 " --> pdb=" O   GLU A 962 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 967 through 968
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1014 through 1016
      removed outlier: 3.569A  pdb=" N   PHE A1015 " --> pdb=" O   ILE A1023 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 736 through 737
      removed outlier: 3.614A  pdb=" N   GLN B 804 " --> pdb=" O   ILE B 780 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.894A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 913
      removed outlier: 3.520A  pdb=" N   SER B 919 " --> pdb=" O   ASN B1007 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 922 through 926
      removed outlier: 6.145A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE B 931 " --> pdb=" O   SER B 926 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B 974 " --> pdb=" O   ILE B 934 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS B 977 " --> pdb=" O   GLU B 962 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 967 through 968
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1014 through 1016
      removed outlier: 3.569A  pdb=" N   PHE B1015 " --> pdb=" O   ILE B1023 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    900 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2524
        1.35 -     1.46: 1914
        1.46 -     1.58: 3568
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 8044
  Sorted by residual:
  bond pdb=" C   SER B1162 "
       pdb=" N   PRO B1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.45e+00
  bond pdb=" C   SER A1162 "
       pdb=" N   PRO A1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.028 2.34e-02 1.83e+03 1.39e+00
  bond pdb=" C   LEU A1036 "
       pdb=" N   PRO A1037 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.28e-02 6.10e+03 5.00e-01
  bond pdb=" N   THR A1123 "
       pdb=" CA  THR A1123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.470 -0.012 1.77e-02 3.19e+03 4.31e-01
  bond pdb=" N   LEU B1126 "
       pdb=" CA  LEU B1126 "
    ideal  model  delta    sigma   weight residual
    1.462  1.471 -0.009 1.48e-02 4.57e+03 3.93e-01
  ... (remaining 8039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 10732
        1.88 -     3.77: 118
        3.77 -     5.65: 14
        5.65 -     7.54: 4
        7.54 -     9.42: 6
  Bond angle restraints: 10874
  Sorted by residual:
  angle pdb=" C   HIS B1099 "
        pdb=" N   THR B1100 "
        pdb=" CA  THR B1100 "
      ideal   model   delta    sigma   weight residual
     121.54  127.07   -5.53 1.91e+00 2.74e-01 8.37e+00
  angle pdb=" C   HIS A1099 "
        pdb=" N   THR A1100 "
        pdb=" CA  THR A1100 "
      ideal   model   delta    sigma   weight residual
     121.54  127.04   -5.50 1.91e+00 2.74e-01 8.29e+00
  angle pdb=" CA  LEU B1126 "
        pdb=" CB  LEU B1126 "
        pdb=" CG  LEU B1126 "
      ideal   model   delta    sigma   weight residual
     116.30  125.72   -9.42 3.50e+00 8.16e-02 7.24e+00
  angle pdb=" CA  LEU A1159 "
        pdb=" CB  LEU A1159 "
        pdb=" CG  LEU A1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.71   -9.41 3.50e+00 8.16e-02 7.23e+00
  angle pdb=" CA  LEU B1159 "
        pdb=" CB  LEU B1159 "
        pdb=" CG  LEU B1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  ... (remaining 10869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.38: 4190
       10.38 -    20.76: 409
       20.76 -    31.15: 161
       31.15 -    41.53: 72
       41.53 -    51.91: 18
  Dihedral angle restraints: 4850
    sinusoidal: 2026
      harmonic: 2824
  Sorted by residual:
  dihedral pdb=" CA  THR B1123 "
           pdb=" C   THR B1123 "
           pdb=" N   TYR B1124 "
           pdb=" CA  TYR B1124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  THR A1123 "
           pdb=" C   THR A1123 "
           pdb=" N   TYR A1124 "
           pdb=" CA  TYR A1124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PRO B 938 "
           pdb=" C   PRO B 938 "
           pdb=" N   LEU B 939 "
           pdb=" CA  LEU B 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.22  -15.78     0      5.00e+00 4.00e-02 9.96e+00
  ... (remaining 4847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 737
       0.030 -    0.060: 279
       0.060 -    0.089: 89
       0.089 -    0.119: 48
       0.119 -    0.149: 7
  Chirality restraints: 1160
  Sorted by residual:
  chirality pdb=" CA  LEU B 865 "
            pdb=" N   LEU B 865 "
            pdb=" C   LEU B 865 "
            pdb=" CB  LEU B 865 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  LEU A 865 "
            pdb=" N   LEU A 865 "
            pdb=" C   LEU A 865 "
            pdb=" CB  LEU A 865 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE A1125 "
            pdb=" N   ILE A1125 "
            pdb=" C   ILE A1125 "
            pdb=" CB  ILE A1125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1157 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 769 "    0.011 2.00e-02 2.50e+03   1.16e-02 2.69e+00
        pdb=" CG  TYR A 769 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 769 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 769 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 769 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 769 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 769 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 769 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 769 "    0.010 2.00e-02 2.50e+03   1.14e-02 2.61e+00
        pdb=" CG  TYR B 769 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 769 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 769 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 769 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 769 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 769 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 769 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.99e+00
        pdb=" N   PRO B 938 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 472
        2.74 -     3.28: 8024
        3.28 -     3.82: 12438
        3.82 -     4.36: 14640
        4.36 -     4.90: 24614
  Nonbonded interactions: 60188
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1109 "
            pdb=" OE1 GLU A1112 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B1109 "
            pdb=" OE1 GLU B1112 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER A 953 "
            pdb=" OD1 ASN A 955 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER B 953 "
            pdb=" OD1 ASN B 955 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.298 3.040
  ... (remaining 60183 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'
  selection = chain 'B'
}

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:             4.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.710
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5888
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      :  0.002   0.028   8044  Z= 0.109
  Angle     :  0.540   9.420  10874  Z= 0.276
  Chirality :  0.039   0.149   1160
  Planarity :  0.003   0.035   1388
  Dihedral  : 10.980  51.912   3038
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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: -0.40 (0.27), residues: 950
  helix:  0.14 (0.27), residues: 380
  sheet:  1.65 (0.63), residues: 78
  loop : -0.88 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 861 
 HIS   0.002   0.000   HIS B1099 
 PHE   0.008   0.001   PHE B 913 
 TYR   0.029   0.001   TYR A 769 
 ARG   0.001   0.000   ARG B 863 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  959 PHE cc_start: 0.8113 (m-80) cc_final: 0.7725 (m-80)
REVERT: A  990 PHE cc_start: 0.6724 (m-80) cc_final: 0.6240 (m-10)
REVERT: B  957 MET cc_start: 0.8326 (mmp) cc_final: 0.8029 (mmp)
REVERT: B  959 PHE cc_start: 0.8252 (m-80) cc_final: 0.7851 (m-80)
REVERT: B  990 PHE cc_start: 0.6862 (m-80) cc_final: 0.6437 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1745
  time to fit residues: 21.7549
Evaluate side-chains
  69 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0970
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 930 ASN
A1007 ASN
B 930 ASN
B1007 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6052
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8044  Z= 0.172
  Angle     :  0.571   8.685  10874  Z= 0.291
  Chirality :  0.042   0.140   1160
  Planarity :  0.004   0.033   1388
  Dihedral  :  3.924  18.746   1072
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  7.23 %
    Favored  : 91.82 %
  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:  0.28 (0.27), residues: 950
  helix:  1.16 (0.27), residues: 390
  sheet:  0.97 (0.63), residues: 78
  loop : -0.76 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 820 
 HIS   0.005   0.001   HIS B1099 
 PHE   0.021   0.001   PHE B 913 
 TYR   0.021   0.002   TYR A 769 
 ARG   0.004   0.000   ARG A 873 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: A  957 MET cc_start: 0.8659 (mmp) cc_final: 0.8322 (mmp)
REVERT: A  990 PHE cc_start: 0.6866 (m-80) cc_final: 0.6148 (m-80)
REVERT: B  756 MET cc_start: 0.6816 (tpp) cc_final: 0.6576 (tpp)
REVERT: B  957 MET cc_start: 0.8613 (mmp) cc_final: 0.8366 (mmm)
REVERT: B  959 PHE cc_start: 0.8268 (m-80) cc_final: 0.7794 (m-80)
REVERT: B  990 PHE cc_start: 0.6899 (m-80) cc_final: 0.6217 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 77
  average time/residue: 0.1653
  time to fit residues: 18.9501
Evaluate side-chains
  71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue 1053 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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: 0.6087
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8044  Z= 0.148
  Angle     :  0.538   8.723  10874  Z= 0.270
  Chirality :  0.041   0.146   1160
  Planarity :  0.003   0.032   1388
  Dihedral  :  3.921  20.814   1072
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.48 %
    Favored  : 89.34 %
  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:  0.35 (0.28), residues: 950
  helix:  1.42 (0.27), residues: 390
  sheet:  0.54 (0.60), residues: 78
  loop : -0.81 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B1189 
 HIS   0.004   0.001   HIS B1099 
 PHE   0.010   0.001   PHE A1164 
 TYR   0.011   0.001   TYR A 888 
 ARG   0.002   0.000   ARG B1040 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 1.028 
Fit side-chains
REVERT: A  869 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6500 (mp)
REVERT: A  916 TYR cc_start: 0.7970 (m-80) cc_final: 0.7691 (m-80)
REVERT: A  957 MET cc_start: 0.8719 (mmp) cc_final: 0.8498 (mmm)
REVERT: A  959 PHE cc_start: 0.8201 (m-80) cc_final: 0.7802 (m-80)
REVERT: A  990 PHE cc_start: 0.6961 (m-80) cc_final: 0.6354 (m-80)
REVERT: B  957 MET cc_start: 0.8773 (mmp) cc_final: 0.8367 (mmm)
REVERT: B  990 PHE cc_start: 0.6888 (m-80) cc_final: 0.6285 (m-80)
  outliers start: 10
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1575
  time to fit residues: 19.1132
Evaluate side-chains
  74 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  981 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  981 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.6818

-------------------------------------------------------------------------------
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: 0.6097
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8044  Z= 0.144
  Angle     :  0.527   8.694  10874  Z= 0.264
  Chirality :  0.041   0.147   1160
  Planarity :  0.003   0.034   1388
  Dihedral  :  3.895  21.399   1072
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.95 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.36 (0.28), residues: 950
  helix:  1.54 (0.27), residues: 390
  sheet:  0.31 (0.59), residues: 78
  loop : -0.88 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B1099 
 PHE   0.010   0.001   PHE B 913 
 TYR   0.022   0.001   TYR A 769 
 ARG   0.005   0.000   ARG B1040 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  869 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6299 (mp)
REVERT: A  990 PHE cc_start: 0.6997 (m-80) cc_final: 0.6353 (m-80)
REVERT: B  957 MET cc_start: 0.8774 (mmp) cc_final: 0.8363 (mmm)
REVERT: B  959 PHE cc_start: 0.8152 (m-80) cc_final: 0.7926 (m-80)
REVERT: B  990 PHE cc_start: 0.6960 (m-80) cc_final: 0.6304 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1558
  time to fit residues: 19.8594
Evaluate side-chains
  75 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  981 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  981 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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: 0.6143
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8044  Z= 0.166
  Angle     :  0.557   8.445  10874  Z= 0.276
  Chirality :  0.042   0.150   1160
  Planarity :  0.003   0.034   1388
  Dihedral  :  4.038  22.108   1072
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.09 %
    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:  0.30 (0.27), residues: 950
  helix:  1.52 (0.27), residues: 388
  sheet:  0.17 (0.59), residues: 78
  loop : -0.91 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 861 
 HIS   0.004   0.001   HIS B1099 
 PHE   0.011   0.001   PHE B 809 
 TYR   0.015   0.001   TYR A1029 
 ARG   0.002   0.000   ARG B1131 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  957 MET cc_start: 0.8315 (mmm) cc_final: 0.8008 (mmm)
REVERT: A  990 PHE cc_start: 0.7035 (m-80) cc_final: 0.6635 (m-80)
REVERT: B  957 MET cc_start: 0.8865 (mmp) cc_final: 0.8389 (mmm)
REVERT: B  959 PHE cc_start: 0.8096 (m-80) cc_final: 0.7837 (m-80)
REVERT: B  990 PHE cc_start: 0.7016 (m-80) cc_final: 0.6431 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1468
  time to fit residues: 17.9391
Evaluate side-chains
  76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  981 ASN
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  871 LEU
Chi-restraints excluded: chain B residue  981 ASN
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0070
   chunk 47 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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: 0.6114
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8044  Z= 0.139
  Angle     :  0.530   8.538  10874  Z= 0.263
  Chirality :  0.041   0.151   1160
  Planarity :  0.003   0.035   1388
  Dihedral  :  3.949  22.088   1072
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.15 %
    Favored  : 85.31 %
  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:  0.40 (0.28), residues: 950
  helix:  1.65 (0.27), residues: 388
  sheet:  0.52 (0.56), residues: 88
  loop : -1.00 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B1099 
 PHE   0.007   0.001   PHE A 809 
 TYR   0.023   0.001   TYR A 769 
 ARG   0.003   0.000   ARG A 985 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  957 MET cc_start: 0.8253 (mmm) cc_final: 0.7940 (mmm)
REVERT: A  990 PHE cc_start: 0.7153 (m-80) cc_final: 0.6573 (m-80)
REVERT: A 1097 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.2102 (mt)
REVERT: B  957 MET cc_start: 0.8776 (mmp) cc_final: 0.8285 (mmm)
REVERT: B  959 PHE cc_start: 0.8101 (m-80) cc_final: 0.7813 (m-80)
REVERT: B  990 PHE cc_start: 0.6930 (m-80) cc_final: 0.6337 (m-80)
REVERT: B 1097 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2149 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1431
  time to fit residues: 17.5553
Evaluate side-chains
  76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0270
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7440

-------------------------------------------------------------------------------
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: 0.6144
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8044  Z= 0.156
  Angle     :  0.559   8.862  10874  Z= 0.274
  Chirality :  0.041   0.160   1160
  Planarity :  0.003   0.035   1388
  Dihedral  :  4.019  22.116   1072
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.63 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.24 (0.27), residues: 950
  helix:  1.46 (0.27), residues: 400
  sheet:  0.47 (0.56), residues: 88
  loop : -1.10 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 861 
 HIS   0.004   0.001   HIS B1099 
 PHE   0.009   0.001   PHE B 809 
 TYR   0.014   0.001   TYR A 888 
 ARG   0.002   0.000   ARG A 985 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  749 MET cc_start: 0.5831 (mpp) cc_final: 0.5518 (mpp)
REVERT: A  957 MET cc_start: 0.8382 (mmm) cc_final: 0.7982 (mmm)
REVERT: A  959 PHE cc_start: 0.8306 (m-10) cc_final: 0.7980 (m-80)
REVERT: A  990 PHE cc_start: 0.7190 (m-80) cc_final: 0.6553 (m-80)
REVERT: A 1097 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2097 (mt)
REVERT: B  749 MET cc_start: 0.5821 (mpp) cc_final: 0.5508 (mpp)
REVERT: B  957 MET cc_start: 0.8809 (mmp) cc_final: 0.8297 (mmm)
REVERT: B  959 PHE cc_start: 0.8073 (m-80) cc_final: 0.7746 (m-80)
REVERT: B  990 PHE cc_start: 0.6955 (m-80) cc_final: 0.6347 (m-80)
REVERT: B 1097 LEU cc_start: 0.2706 (OUTLIER) cc_final: 0.2124 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1409
  time to fit residues: 17.4496
Evaluate side-chains
  79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  871 LEU
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A1129 GLN
B1129 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8044  Z= 0.135
  Angle     :  0.537   9.014  10874  Z= 0.265
  Chirality :  0.041   0.151   1160
  Planarity :  0.003   0.035   1388
  Dihedral  :  3.938  21.914   1072
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.86 %
    Favored  : 84.24 %
  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:  0.31 (0.27), residues: 950
  helix:  1.54 (0.27), residues: 400
  sheet:  0.44 (0.55), residues: 88
  loop : -1.07 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B1099 
 PHE   0.006   0.001   PHE A 814 
 TYR   0.024   0.001   TYR B 769 
 ARG   0.001   0.000   ARG A 985 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A  749 MET cc_start: 0.6061 (mpp) cc_final: 0.5860 (mpp)
REVERT: A  959 PHE cc_start: 0.8210 (m-10) cc_final: 0.7884 (m-80)
REVERT: A  990 PHE cc_start: 0.7101 (m-80) cc_final: 0.6501 (m-80)
REVERT: A 1097 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2451 (pp)
REVERT: B  957 MET cc_start: 0.8756 (mmp) cc_final: 0.8264 (mmm)
REVERT: B  959 PHE cc_start: 0.8026 (m-80) cc_final: 0.7706 (m-80)
REVERT: B  990 PHE cc_start: 0.6902 (m-80) cc_final: 0.6298 (m-80)
REVERT: B 1097 LEU cc_start: 0.2705 (OUTLIER) cc_final: 0.2136 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1466
  time to fit residues: 18.5952
Evaluate side-chains
  79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  871 LEU
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 79 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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: 0.6166
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8044  Z= 0.168
  Angle     :  0.568   9.563  10874  Z= 0.282
  Chirality :  0.041   0.151   1160
  Planarity :  0.003   0.036   1388
  Dihedral  :  4.141  22.081   1072
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.10 %
    Favored  : 84.12 %
  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:  0.23 (0.27), residues: 950
  helix:  1.46 (0.27), residues: 400
  sheet:  0.35 (0.55), residues: 88
  loop : -1.08 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 861 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.010   0.001   PHE B 809 
 TYR   0.017   0.001   TYR A 888 
 ARG   0.002   0.000   ARG A 985 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  957 MET cc_start: 0.8317 (mmm) cc_final: 0.7574 (mmm)
REVERT: A  959 PHE cc_start: 0.8143 (m-10) cc_final: 0.7793 (m-80)
REVERT: A  990 PHE cc_start: 0.7023 (m-80) cc_final: 0.6476 (m-80)
REVERT: B  749 MET cc_start: 0.5652 (mpp) cc_final: 0.5270 (mpp)
REVERT: B  957 MET cc_start: 0.8863 (mmp) cc_final: 0.8322 (mmm)
REVERT: B  959 PHE cc_start: 0.7972 (m-80) cc_final: 0.7614 (m-80)
REVERT: B  990 PHE cc_start: 0.6852 (m-80) cc_final: 0.6187 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1419
  time to fit residues: 17.9374
Evaluate side-chains
  75 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  871 LEU
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0870
   chunk 45 optimal weight:    0.3980
   chunk 59 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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: 0.6131
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8044  Z= 0.149
  Angle     :  0.566  10.005  10874  Z= 0.278
  Chirality :  0.041   0.154   1160
  Planarity :  0.003   0.035   1388
  Dihedral  :  4.040  22.759   1072
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.69 %
    Favored  : 84.00 %
  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:  0.27 (0.27), residues: 950
  helix:  1.54 (0.27), residues: 400
  sheet:  0.36 (0.55), residues: 88
  loop : -1.10 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 861 
 HIS   0.004   0.001   HIS B1099 
 PHE   0.006   0.001   PHE A 809 
 TYR   0.025   0.001   TYR B 769 
 ARG   0.002   0.000   ARG B 831 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  749 MET cc_start: 0.5956 (mpp) cc_final: 0.5541 (mpp)
REVERT: A  957 MET cc_start: 0.8318 (mmm) cc_final: 0.7568 (mmm)
REVERT: A  959 PHE cc_start: 0.8084 (m-10) cc_final: 0.7728 (m-80)
REVERT: A  990 PHE cc_start: 0.7060 (m-80) cc_final: 0.6497 (m-80)
REVERT: B  749 MET cc_start: 0.5613 (mpp) cc_final: 0.5211 (mpp)
REVERT: B  957 MET cc_start: 0.8828 (mmp) cc_final: 0.8290 (mmm)
REVERT: B  959 PHE cc_start: 0.7932 (m-80) cc_final: 0.7565 (m-80)
REVERT: B  990 PHE cc_start: 0.6904 (m-80) cc_final: 0.6242 (m-80)
  outliers start: 11
  outliers final: 11
  residues processed: 74
  average time/residue: 0.1440
  time to fit residues: 16.8105
Evaluate side-chains
  76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain A residue 1053 VAL
Chi-restraints excluded: chain A residue 1078 HIS
Chi-restraints excluded: chain A residue 1148 MET
Chi-restraints excluded: chain B residue  869 LEU
Chi-restraints excluded: chain B residue  871 LEU
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1053 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1148 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0010
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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 = 0.4521 r_free = 0.4521 target = 0.117855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.102088 restraints weight = 35638.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 5.60
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8044  Z= 0.141
  Angle     :  0.558   9.998  10874  Z= 0.273
  Chirality :  0.041   0.154   1160
  Planarity :  0.003   0.035   1388
  Dihedral  :  3.932  21.078   1072
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.45 %
    Favored  : 84.00 %
  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:  0.34 (0.28), residues: 950
  helix:  1.59 (0.27), residues: 400
  sheet:  0.42 (0.55), residues: 88
  loop : -1.08 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 861 
 HIS   0.004   0.001   HIS B1099 
 PHE   0.006   0.001   PHE B 809 
 TYR   0.021   0.001   TYR A 888 
 ARG   0.001   0.000   ARG B1141 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1753.33 seconds
wall clock time: 33 minutes 4.83 seconds (1984.83 seconds total)