Starting phenix.real_space_refine
on Wed Mar 12 17:36:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gvc_34290/03_2025/8gvc_34290_trim.cif"
  }
  resolution = 2.89
  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=   0.165
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      46      5.16       5
     C    5372      2.51       5
     N    1326      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8080
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.92, per 1000 atoms: 0.73
  Number of scatterers: 8080
  At special positions: 0
  Unit cell: (89.1, 129.8, 81.4, 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      46     16.00
     O    1336      8.00
     N    1326      7.00
     C    5372      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: 2.35
  Conformation dependent library (CDL) restraints added in 979.6 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      73.1% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 696 through 702
      removed outlier: 3.801A  pdb=" N   PHE A 700 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 734
      removed outlier: 3.626A  pdb=" N   LEU A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   PHE A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA A 718 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 740 through 758
    Processing helix  chain 'A' and resid 768 through 784
    Processing helix  chain 'A' and resid 791 through 810
      removed outlier: 4.196A  pdb=" N   TRP A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE A 796 " --> pdb=" O   GLY A 792 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY A 797 " --> pdb=" O   ARG A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 819
      removed outlier: 3.857A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 4.107A  pdb=" N   ILE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 845 " --> pdb=" O   TYR A 841 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A 846 " --> pdb=" O   LYS A 842 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 923
      removed outlier: 3.646A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 937
    Processing helix  chain 'A' and resid 938 through 954
      removed outlier: 3.684A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 976
      removed outlier: 3.708A  pdb=" N   ARG A 976 " --> pdb=" O   PRO A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 997
      removed outlier: 3.713A  pdb=" N   VAL A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1020
    Processing helix  chain 'A' and resid 1033 through 1047
      removed outlier: 3.570A  pdb=" N   ALA A1047 " --> pdb=" O   GLY A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1050
      No H-bonds generated for 'chain 'A' and resid 1048 through 1050'
    Processing helix  chain 'A' and resid 1057 through 1066
    Processing helix  chain 'A' and resid 1091 through 1102
    Processing helix  chain 'A' and resid 1109 through 1113
      removed outlier: 3.659A  pdb=" N   ILE A1113 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1129
      removed outlier: 3.883A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A1121 " --> pdb=" O   VAL A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1141
      removed outlier: 3.660A  pdb=" N   HIS A1140 " --> pdb=" O   TYR A1136 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A1141 " --> pdb=" O   GLU A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.762A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 3.567A  pdb=" N   LYS A1156 " --> pdb=" O   VAL A1152 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS A1157 " --> pdb=" O   THR A1153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1152 through 1157'
    Processing helix  chain 'A' and resid 1159 through 1183
    Processing helix  chain 'A' and resid 1185 through 1187
      No H-bonds generated for 'chain 'A' and resid 1185 through 1187'
    Processing helix  chain 'A' and resid 1188 through 1195
    Processing helix  chain 'A' and resid 1195 through 1208
      removed outlier: 3.996A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1217
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 696 through 702
      removed outlier: 3.816A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.637A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   PHE B 717 " --> pdb=" O   ILE B 713 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 718 " --> pdb=" O   PHE B 714 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
    Processing helix  chain 'B' and resid 740 through 758
    Processing helix  chain 'B' and resid 768 through 786
    Processing helix  chain 'B' and resid 788 through 810
      removed outlier: 3.877A  pdb=" N   GLY B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG B 793 " --> pdb=" O   TYR B 789 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 819
      removed outlier: 3.971A  pdb=" N   PHE B 814 " --> pdb=" O   GLU B 811 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 850
      removed outlier: 4.099A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU B 843 " --> pdb=" O   THR B 839 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 844 " --> pdb=" O   PHE B 840 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS B 845 " --> pdb=" O   TYR B 841 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE B 846 " --> pdb=" O   LYS B 842 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 900 through 923
      removed outlier: 3.517A  pdb=" N   LEU B 905 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 937
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.661A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 976
      removed outlier: 3.700A  pdb=" N   ARG B 976 " --> pdb=" O   PRO B 973 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 991 through 997
      removed outlier: 3.837A  pdb=" N   VAL B 995 " --> pdb=" O   VAL B 991 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1019
    Processing helix  chain 'B' and resid 1033 through 1047
      removed outlier: 3.534A  pdb=" N   ALA B1047 " --> pdb=" O   GLY B1043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1050
      No H-bonds generated for 'chain 'B' and resid 1048 through 1050'
    Processing helix  chain 'B' and resid 1058 through 1066
    Processing helix  chain 'B' and resid 1091 through 1102
    Processing helix  chain 'B' and resid 1109 through 1113
      removed outlier: 3.637A  pdb=" N   ILE B1113 " --> pdb=" O   LEU B1110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1114 through 1129
      removed outlier: 3.883A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1133 through 1141
      removed outlier: 3.726A  pdb=" N   LEU B1141 " --> pdb=" O   GLU B1137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.589A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.612A  pdb=" N   LYS B1156 " --> pdb=" O   VAL B1152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1159 through 1183
    Processing helix  chain 'B' and resid 1185 through 1187
      No H-bonds generated for 'chain 'B' and resid 1185 through 1187'
    Processing helix  chain 'B' and resid 1188 through 1195
    Processing helix  chain 'B' and resid 1195 through 1208
      removed outlier: 3.933A  pdb=" N   LEU B1204 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   THR B1205 " --> pdb=" O   MET B1201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1209 through 1217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766
      removed outlier: 3.527A  pdb=" N   ALA A1055 " --> pdb=" O   GLY A 766 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071
    Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766
      removed outlier: 3.618A  pdb=" N   ALA B1055 " --> pdb=" O   GLY B 766 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1070 through 1071
      removed outlier: 3.507A  pdb=" N   GLU B1085 " --> pdb=" O   VAL B1070 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1368 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: 2.31

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2224
        1.33 -     1.45: 1259
        1.45 -     1.57: 4717
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 8278
  Sorted by residual:
  bond pdb=" C   BCT B1301 "
       pdb=" O3  BCT B1301 "
    ideal  model  delta    sigma   weight residual
    1.389  1.311  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C   BCT A1301 "
       pdb=" O3  BCT A1301 "
    ideal  model  delta    sigma   weight residual
    1.389  1.311  0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" CA  SER B 768 "
       pdb=" C   SER B 768 "
    ideal  model  delta    sigma   weight residual
    1.521  1.506  0.015 1.20e-02 6.94e+03 1.64e+00
  bond pdb=" C   BCT A1301 "
       pdb=" O2  BCT A1301 "
    ideal  model  delta    sigma   weight residual
    1.241  1.217  0.024 2.00e-02 2.50e+03 1.49e+00
  bond pdb=" CA  SER A 768 "
       pdb=" C   SER A 768 "
    ideal  model  delta    sigma   weight residual
    1.521  1.507  0.014 1.20e-02 6.94e+03 1.44e+00
  ... (remaining 8273 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 11152
        2.42 -     4.84: 70
        4.84 -     7.26: 7
        7.26 -     9.68: 1
        9.68 -    12.10: 2
  Bond angle restraints: 11232
  Sorted by residual:
  angle pdb=" N   VAL B 948 "
        pdb=" CA  VAL B 948 "
        pdb=" C   VAL B 948 "
      ideal   model   delta    sigma   weight residual
     110.72  104.86    5.86 1.01e+00 9.80e-01 3.36e+01
  angle pdb=" N   VAL A 948 "
        pdb=" CA  VAL A 948 "
        pdb=" C   VAL A 948 "
      ideal   model   delta    sigma   weight residual
     110.72  104.87    5.85 1.01e+00 9.80e-01 3.36e+01
  angle pdb=" N   ILE A 946 "
        pdb=" CA  ILE A 946 "
        pdb=" C   ILE A 946 "
      ideal   model   delta    sigma   weight residual
     110.42  114.55   -4.13 9.60e-01 1.09e+00 1.85e+01
  angle pdb=" N   ILE B 946 "
        pdb=" CA  ILE B 946 "
        pdb=" C   ILE B 946 "
      ideal   model   delta    sigma   weight residual
     110.42  114.52   -4.10 9.60e-01 1.09e+00 1.82e+01
  angle pdb=" O1  BCT B1301 "
        pdb=" C   BCT B1301 "
        pdb=" O2  BCT B1301 "
      ideal   model   delta    sigma   weight residual
     129.92  117.82   12.10 3.00e+00 1.11e-01 1.63e+01
  ... (remaining 11227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 4266
       16.11 -    32.22: 482
       32.22 -    48.33: 115
       48.33 -    64.45: 24
       64.45 -    80.56: 7
  Dihedral angle restraints: 4894
    sinusoidal: 1950
      harmonic: 2944
  Sorted by residual:
  dihedral pdb=" CG  ARG B 691 "
           pdb=" CD  ARG B 691 "
           pdb=" NE  ARG B 691 "
           pdb=" CZ  ARG B 691 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.33   42.67     2      1.50e+01 4.44e-03 9.80e+00
  dihedral pdb=" CG  ARG A 691 "
           pdb=" CD  ARG A 691 "
           pdb=" NE  ARG A 691 "
           pdb=" CZ  ARG A 691 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.42   42.58     2      1.50e+01 4.44e-03 9.77e+00
  dihedral pdb=" CB  MET B 745 "
           pdb=" CG  MET B 745 "
           pdb=" SD  MET B 745 "
           pdb=" CE  MET B 745 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.30  -59.70     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 4891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1006
       0.039 -    0.077: 252
       0.077 -    0.116: 62
       0.116 -    0.154: 9
       0.154 -    0.193: 1
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CA  GLU A 955 "
            pdb=" N   GLU A 955 "
            pdb=" C   GLU A 955 "
            pdb=" CB  GLU A 955 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CA  VAL B 964 "
            pdb=" N   VAL B 964 "
            pdb=" C   VAL B 964 "
            pdb=" CB  VAL B 964 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  ILE A 946 "
            pdb=" N   ILE A 946 "
            pdb=" C   ILE A 946 "
            pdb=" CB  ILE A 946 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.31    0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   BCT B1301 "    0.064 2.00e-02 2.50e+03   3.69e-02 1.36e+01
        pdb=" O1  BCT B1301 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2  BCT B1301 "   -0.022 2.00e-02 2.50e+03
        pdb=" O3  BCT B1301 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   BCT A1301 "    0.033 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" O1  BCT A1301 "   -0.012 2.00e-02 2.50e+03
        pdb=" O2  BCT A1301 "   -0.011 2.00e-02 2.50e+03
        pdb=" O3  BCT A1301 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 693 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.72e+00
        pdb=" N   PRO B 694 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 694 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 694 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.32: 10
        2.32 -     2.96: 3948
        2.96 -     3.61: 11248
        3.61 -     4.25: 16924
        4.25 -     4.90: 29953
  Nonbonded interactions: 62083
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 820 "
            pdb=" CZ  ARG A1200 "
     model   vdw
     1.670 3.270
  nonbonded pdb=" OG  SER A 820 "
            pdb=" NE  ARG A1200 "
     model   vdw
     1.925 3.120
  nonbonded pdb=" O   ALA B1057 "
            pdb=" OG1 THR B1058 "
     model   vdw
     2.031 3.040
  nonbonded pdb=" O   ASP A 956 "
            pdb=" OD1 ASP A 956 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OD1 ASP A1151 "
            pdb=" NZ  LYS A1156 "
     model   vdw
     2.148 3.120
  ... (remaining 62078 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: 0.04
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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.600
  Find NCS groups from input model:        0.300
  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:             0.010
  Load rotamer database and sin/cos tables:15.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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   0.078   8278  Z= 0.173
  Angle     :  0.481  12.101  11232  Z= 0.267
  Chirality :  0.036   0.193   1330
  Planarity :  0.003   0.041   1380
  Dihedral  : 14.663  80.557   2990
  Min Nonbonded Distance : 1.670

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.97 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.10 %
    Favored  : 85.76 %
  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:  2.06 (0.28), residues: 1014
  helix:  2.37 (0.22), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 795 
 HIS   0.002   0.001   HIS A1149 
 PHE   0.008   0.001   PHE B 938 
 TYR   0.007   0.001   TYR B1124 
 ARG   0.009   0.000   ARG B1206 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6906 (mtp180)
REVERT: A 1163 MET cc_start: 0.7431 (ttp) cc_final: 0.6840 (ttp)
REVERT: B 1205 THR cc_start: 0.8454 (m) cc_final: 0.8070 (p)
REVERT: B 1206 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6710 (ttp-170)
  outliers start: 10
  outliers final: 9
  residues processed: 132
  average time/residue: 1.3018
  time to fit residues: 181.5393
Evaluate side-chains
  125 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1209 THR
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1183 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.160608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117920 restraints weight = 8369.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.93
r_work: 0.3290 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.0928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8278  Z= 0.195
  Angle     :  0.534   8.626  11232  Z= 0.271
  Chirality :  0.039   0.138   1330
  Planarity :  0.005   0.055   1380
  Dihedral  :  3.926  24.207   1105
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.76 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.55 %
    Favored  : 84.62 %
  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:  1.98 (0.28), residues: 1014
  helix:  2.29 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.61 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.012   0.001   PHE B 774 
 TYR   0.009   0.001   TYR A1124 
 ARG   0.006   0.000   ARG B1206 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.6907 (mtm110) cc_final: 0.6567 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6710 (mp0) cc_final: 0.6308 (mp0)
REVERT: B 1206 ARG cc_start: 0.7481 (mtm110) cc_final: 0.6936 (ttp-170)
  outliers start: 16
  outliers final: 9
  residues processed: 128
  average time/residue: 1.5000
  time to fit residues: 202.3135
Evaluate side-chains
  118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0770
   chunk 19 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.0742

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.154716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.112925 restraints weight = 8508.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.98
r_work: 0.3313 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8278  Z= 0.229
  Angle     :  0.531   8.780  11232  Z= 0.272
  Chirality :  0.040   0.146   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.664  21.905   1097
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.66 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.35 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.27), residues: 1014
  helix:  2.17 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.69 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.013   0.001   TYR B1124 
 ARG   0.003   0.000   ARG B 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7005 (mtm110) cc_final: 0.6668 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6840 (mp0) cc_final: 0.6405 (mp0)
REVERT: B 1023 GLU cc_start: 0.7177 (mp0) cc_final: 0.6752 (mp0)
REVERT: B 1071 MET cc_start: 0.8214 (mmm) cc_final: 0.7980 (mmt)
REVERT: B 1206 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7002 (ttp-170)
  outliers start: 17
  outliers final: 9
  residues processed: 121
  average time/residue: 1.3974
  time to fit residues: 178.9655
Evaluate side-chains
  115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 62 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.153175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.110262 restraints weight = 8402.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.97
r_work: 0.3276 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8278  Z= 0.227
  Angle     :  0.530  10.555  11232  Z= 0.268
  Chirality :  0.039   0.145   1330
  Planarity :  0.005   0.058   1380
  Dihedral  :  3.697  20.865   1097
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.76 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.58 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.27), residues: 1014
  helix:  2.11 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.74 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.012   0.001   TYR B1124 
 ARG   0.004   0.000   ARG A 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7041 (mtm110) cc_final: 0.6729 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6969 (mp0) cc_final: 0.6438 (mp0)
REVERT: B  895 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7016 (ttm110)
REVERT: B 1023 GLU cc_start: 0.7296 (mp0) cc_final: 0.6838 (mp0)
REVERT: B 1141 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8367 (mp)
REVERT: B 1206 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7029 (ttp-170)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 1.5962
  time to fit residues: 201.4660
Evaluate side-chains
  118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1141 LEU
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.151944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.109660 restraints weight = 8370.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.98
r_work: 0.3214 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8278  Z= 0.256
  Angle     :  0.545   8.614  11232  Z= 0.277
  Chirality :  0.040   0.154   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.781  20.734   1097
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.86 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.15 %
    Favored  : 82.00 %
  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:  1.64 (0.27), residues: 1014
  helix:  2.05 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.80 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.013   0.001   TYR B1124 
 ARG   0.004   0.000   ARG A 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6703 (mtm110)
REVERT: A 1023 GLU cc_start: 0.7024 (mp0) cc_final: 0.6476 (mp0)
REVERT: A 1082 LYS cc_start: 0.6662 (pttm) cc_final: 0.6289 (ptmm)
REVERT: B  895 ARG cc_start: 0.7604 (mpt-90) cc_final: 0.6985 (ttm110)
REVERT: B 1023 GLU cc_start: 0.7322 (mp0) cc_final: 0.6853 (mp0)
REVERT: B 1141 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8279 (mp)
REVERT: B 1206 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7055 (ttp-170)
  outliers start: 25
  outliers final: 15
  residues processed: 127
  average time/residue: 1.9401
  time to fit residues: 261.4247
Evaluate side-chains
  119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1194 ILE
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1141 LEU
Chi-restraints excluded: chain B residue 1194 ILE
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.154771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111848 restraints weight = 8373.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.00
r_work: 0.3288 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8278  Z= 0.181
  Angle     :  0.504  10.704  11232  Z= 0.253
  Chirality :  0.038   0.139   1330
  Planarity :  0.004   0.057   1380
  Dihedral  :  3.648  18.348   1097
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.96 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.29 %
    Favored  : 82.00 %
  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:  1.79 (0.27), residues: 1014
  helix:  2.17 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.76 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.008   0.001   TYR B1124 
 ARG   0.003   0.000   ARG A 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7018 (mtm110) cc_final: 0.6712 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6954 (mp0) cc_final: 0.6360 (mp0)
REVERT: A 1082 LYS cc_start: 0.6666 (pttm) cc_final: 0.6302 (ptmm)
REVERT: A 1211 ARG cc_start: 0.7154 (ttt90) cc_final: 0.6534 (tpt170)
REVERT: B  895 ARG cc_start: 0.7567 (mpt-90) cc_final: 0.6925 (ttm110)
REVERT: B 1023 GLU cc_start: 0.7288 (mp0) cc_final: 0.6799 (mp0)
REVERT: B 1206 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7130 (ttp-170)
  outliers start: 15
  outliers final: 10
  residues processed: 130
  average time/residue: 1.3781
  time to fit residues: 188.8105
Evaluate side-chains
  115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1206 ARG
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0070
   chunk 69 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.155215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.113477 restraints weight = 8405.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.99
r_work: 0.3324 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8278  Z= 0.177
  Angle     :  0.507  10.488  11232  Z= 0.251
  Chirality :  0.038   0.140   1330
  Planarity :  0.004   0.057   1380
  Dihedral  :  3.597  17.319   1097
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.76 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.97 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.27), residues: 1014
  helix:  2.23 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.75 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.006   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.005   0.000   ARG B 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6709 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6977 (mp0) cc_final: 0.6444 (mp0)
REVERT: A 1082 LYS cc_start: 0.6655 (pttm) cc_final: 0.6287 (ptmm)
REVERT: B 1023 GLU cc_start: 0.7275 (mp0) cc_final: 0.6776 (mp0)
REVERT: B 1071 MET cc_start: 0.8258 (mmm) cc_final: 0.8049 (mmt)
REVERT: B 1206 ARG cc_start: 0.7480 (mtm110) cc_final: 0.7130 (ttp-170)
  outliers start: 19
  outliers final: 13
  residues processed: 120
  average time/residue: 1.3771
  time to fit residues: 174.5376
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1194 ILE
Chi-restraints excluded: chain A residue 1206 ARG
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1194 ILE
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.170012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129419 restraints weight = 8355.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.85
r_work: 0.3373 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8278  Z= 0.174
  Angle     :  0.500   9.624  11232  Z= 0.248
  Chirality :  0.038   0.138   1330
  Planarity :  0.004   0.057   1380
  Dihedral  :  3.552  17.234   1096
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.96 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.88 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 1014
  helix:  2.25 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.73 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 795 
 HIS   0.006   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.009   0.001   TYR B1124 
 ARG   0.004   0.000   ARG A 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6711 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6868 (mp0) cc_final: 0.6239 (mp0)
REVERT: B  687 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6768 (mtm110)
REVERT: B 1023 GLU cc_start: 0.7285 (mp0) cc_final: 0.6780 (mp0)
REVERT: B 1071 MET cc_start: 0.8250 (mmm) cc_final: 0.8021 (mmt)
REVERT: B 1206 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7144 (ttp-170)
  outliers start: 14
  outliers final: 9
  residues processed: 117
  average time/residue: 1.4771
  time to fit residues: 182.5790
Evaluate side-chains
  114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1194 ILE
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 100 optimal weight:    0.4980
   chunk 14 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0020
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.171767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.131928 restraints weight = 8424.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.72
r_work: 0.3364 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8278  Z= 0.156
  Angle     :  0.489   9.260  11232  Z= 0.242
  Chirality :  0.038   0.134   1330
  Planarity :  0.004   0.057   1380
  Dihedral  :  3.484  17.096   1096
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.86 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 17.77 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.27), residues: 1014
  helix:  2.32 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.67 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.006   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.008   0.001   TYR A1124 
 ARG   0.005   0.000   ARG A 933 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.6968 (mtm110) cc_final: 0.6676 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6830 (mp0) cc_final: 0.6285 (mp0)
REVERT: A 1214 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7427 (mmmt)
REVERT: B  687 ARG cc_start: 0.6938 (mtm110) cc_final: 0.6735 (mtm110)
REVERT: B 1023 GLU cc_start: 0.7257 (mp0) cc_final: 0.6749 (mp0)
REVERT: B 1071 MET cc_start: 0.8287 (mmm) cc_final: 0.8066 (mmt)
REVERT: B 1200 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7148 (tmt-80)
  outliers start: 13
  outliers final: 11
  residues processed: 121
  average time/residue: 1.4322
  time to fit residues: 182.3293
Evaluate side-chains
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1194 ILE
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1194 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 87 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.158611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117994 restraints weight = 8402.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.95
r_work: 0.3307 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8278  Z= 0.192
  Angle     :  0.523  10.513  11232  Z= 0.255
  Chirality :  0.038   0.141   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.539  17.110   1096
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.86 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.77 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.27), residues: 1014
  helix:  2.30 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.69 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.005   0.000   ARG B 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.6977 (mtm110) cc_final: 0.6696 (mtm110)
REVERT: A 1023 GLU cc_start: 0.6926 (mp0) cc_final: 0.6350 (mp0)
REVERT: A 1214 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7444 (mmmt)
REVERT: B  690 ARG cc_start: 0.7113 (mtt90) cc_final: 0.6536 (mtm110)
REVERT: B 1023 GLU cc_start: 0.7305 (mp0) cc_final: 0.6679 (mp0)
REVERT: B 1200 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7170 (tmt-80)
  outliers start: 12
  outliers final: 11
  residues processed: 116
  average time/residue: 1.6326
  time to fit residues: 200.1540
Evaluate side-chains
  116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1194 ILE
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1194 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 34 optimal weight:    0.1980
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.162097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.120359 restraints weight = 8417.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 1.94
r_work: 0.3333 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8278  Z= 0.167
  Angle     :  0.512   9.849  11232  Z= 0.250
  Chirality :  0.038   0.135   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.523  17.026   1096
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.16 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.88 %
    Favored  : 80.52 %
  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:  2.00 (0.27), residues: 1014
  helix:  2.33 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.66 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 795 
 HIS   0.006   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.008   0.001   TYR A1124 
 ARG   0.014   0.001   ARG B 687 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6713.86 seconds
wall clock time: 118 minutes 48.17 seconds (7128.17 seconds total)