Starting phenix.real_space_refine
on Sun May 11 14:14:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gvf_34292/05_2025/8gvf_34292.cif"
  }
  resolution = 3.09
  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=   0.002 sd=   0.145
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    5370      2.51       5
     N    1326      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8072
  Number of models: 1
  Model: ""
    Number of chains: 2
    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
  Time building chain proxies: 5.07, per 1000 atoms: 0.63
  Number of scatterers: 8072
  At special positions: 0
  Unit cell: (84.7, 135.3, 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    1330      8.00
     N    1326      7.00
     C    5370      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: 1.91
  Conformation dependent library (CDL) restraints added in 997.5 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:
      58 helices and 4 sheets defined
      73.6% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 696 through 702
      removed outlier: 3.536A  pdb=" N   PHE A 700 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 734
      removed outlier: 3.606A  pdb=" N   LEU A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 3.783A  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
      removed outlier: 3.569A  pdb=" N   LEU A 772 " --> pdb=" O   SER A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 810
      removed outlier: 4.175A  pdb=" N   TRP A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE A 796 " --> pdb=" O   GLY A 792 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLY A 797 " --> pdb=" O   ARG A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 818
      removed outlier: 3.758A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE A 818 " --> pdb=" O   LEU A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 3.529A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ILE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS A 845 " --> pdb=" O   TYR A 841 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ILE A 846 " --> pdb=" O   LYS A 842 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 921
      removed outlier: 3.507A  pdb=" N   SER A 904 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 924
      No H-bonds generated for 'chain 'A' and resid 922 through 924'
    Processing helix  chain 'A' and resid 928 through 938
    Processing helix  chain 'A' and resid 938 through 954
      removed outlier: 3.781A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 976
      removed outlier: 3.928A  pdb=" N   ARG A 976 " --> pdb=" O   PRO A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 997
      removed outlier: 3.694A  pdb=" N   MET A 994 " --> pdb=" O   PRO A 990 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1020
      removed outlier: 3.579A  pdb=" N   ALA A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A1003 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1047
    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: 3.691A  pdb=" N   ILE A1113 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1129
      removed outlier: 4.034A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY A1120 " --> pdb=" O   ALA A1116 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A1121 " --> pdb=" O   VAL A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1141
      removed outlier: 3.687A  pdb=" N   LEU A1141 " --> pdb=" O   GLU A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.945A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 3.729A  pdb=" N   LYS A1156 " --> pdb=" O   VAL A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1183
      removed outlier: 3.522A  pdb=" N   MET A1181 " --> pdb=" O   LEU A1177 " (cutoff:3.500A)
    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: 3.562A  pdb=" N   LEU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A1201 " --> pdb=" O   VAL A1197 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1217
      removed outlier: 3.640A  pdb=" N   CYS A1215 " --> pdb=" O   ARG A1211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 696 through 702
      removed outlier: 3.561A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.618A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE B 717 " --> pdb=" O   ILE B 713 " (cutoff:3.500A)
      removed outlier: 3.784A  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
      removed outlier: 3.518A  pdb=" N   LEU B 772 " --> pdb=" O   SER B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 788 through 810
      removed outlier: 4.139A  pdb=" N   GLY B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG B 793 " --> pdb=" O   TYR B 789 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 818
      removed outlier: 3.897A  pdb=" N   PHE B 814 " --> pdb=" O   GLU B 811 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 850
      removed outlier: 3.531A  pdb=" N   GLN B 824 " --> pdb=" O   SER B 820 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU B 843 " --> pdb=" O   THR B 839 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 844 " --> pdb=" O   PHE B 840 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B 845 " --> pdb=" O   TYR B 841 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE B 846 " --> pdb=" O   LYS B 842 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 900 through 921
      removed outlier: 3.647A  pdb=" N   LEU B 905 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 924
      No H-bonds generated for 'chain 'B' and resid 922 through 924'
    Processing helix  chain 'B' and resid 928 through 938
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.787A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 976
      removed outlier: 3.890A  pdb=" N   ARG B 976 " --> pdb=" O   PRO B 973 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 990 through 997
      removed outlier: 3.789A  pdb=" N   MET B 994 " --> pdb=" O   PRO B 990 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL B 995 " --> pdb=" O   VAL B 991 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1020
      removed outlier: 3.550A  pdb=" N   ALA B1001 " --> pdb=" O   SER B 997 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU B1003 " --> pdb=" O   LEU B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1047
    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: 3.650A  pdb=" N   ILE B1113 " --> pdb=" O   LEU B1110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1114 through 1129
      removed outlier: 4.058A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B1120 " --> pdb=" O   ALA B1116 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1133 through 1141
      removed outlier: 3.692A  pdb=" N   LEU B1141 " --> pdb=" O   GLU B1137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.758A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.814A  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: 4.018A  pdb=" N   LEU B1204 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 5.367A  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: 3.622A  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
      removed outlier: 6.810A  pdb=" N   VAL A1070 " --> pdb=" O   GLN A1084 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766
      removed outlier: 3.593A  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: 6.773A  pdb=" N   VAL B1070 " --> pdb=" O   GLN B1084 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1341 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: 2.16

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2457
        1.34 -     1.46: 1194
        1.46 -     1.57: 4543
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 8272
  Sorted by residual:
  bond pdb=" CG1 ILE A 834 "
       pdb=" CD1 ILE A 834 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.38e+00
  bond pdb=" CA  SER B1103 "
       pdb=" C   SER B1103 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.80e-02 3.09e+03 1.35e+00
  bond pdb=" CA  VAL B 819 "
       pdb=" CB  VAL B 819 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.36e-02 5.41e+03 1.24e+00
  bond pdb=" CG  LYS B1022 "
       pdb=" CD  LYS B1022 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.13e+00
  bond pdb=" N   THR B1058 "
       pdb=" CA  THR B1058 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.08e+00
  ... (remaining 8267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10943
        1.67 -     3.33: 228
        3.33 -     5.00: 43
        5.00 -     6.67: 9
        6.67 -     8.33: 3
  Bond angle restraints: 11226
  Sorted by residual:
  angle pdb=" C   ALA B1057 "
        pdb=" N   THR B1058 "
        pdb=" CA  THR B1058 "
      ideal   model   delta    sigma   weight residual
     121.54  129.87   -8.33 1.91e+00 2.74e-01 1.90e+01
  angle pdb=" C   ALA B1074 "
        pdb=" N   VAL B1075 "
        pdb=" CA  VAL B1075 "
      ideal   model   delta    sigma   weight residual
     121.97  127.85   -5.88 1.80e+00 3.09e-01 1.07e+01
  angle pdb=" CB  LYS A1022 "
        pdb=" CG  LYS A1022 "
        pdb=" CD  LYS A1022 "
      ideal   model   delta    sigma   weight residual
     111.30  118.53   -7.23 2.30e+00 1.89e-01 9.88e+00
  angle pdb=" CB  LYS B1022 "
        pdb=" CG  LYS B1022 "
        pdb=" CD  LYS B1022 "
      ideal   model   delta    sigma   weight residual
     111.30  118.44   -7.14 2.30e+00 1.89e-01 9.64e+00
  angle pdb=" N   LYS A1073 "
        pdb=" CA  LYS A1073 "
        pdb=" C   LYS A1073 "
      ideal   model   delta    sigma   weight residual
     108.19  112.16   -3.97 1.29e+00 6.01e-01 9.47e+00
  ... (remaining 11221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4411
       17.95 -    35.89: 410
       35.89 -    53.84: 56
       53.84 -    71.78: 11
       71.78 -    89.73: 6
  Dihedral angle restraints: 4894
    sinusoidal: 1950
      harmonic: 2944
  Sorted by residual:
  dihedral pdb=" CA  SER B1072 "
           pdb=" C   SER B1072 "
           pdb=" N   LYS B1073 "
           pdb=" CA  LYS B1073 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.38  -19.62     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  SER A 784 "
           pdb=" C   SER A 784 "
           pdb=" N   ASN A 785 "
           pdb=" CA  ASN A 785 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  GLY A1107 "
           pdb=" C   GLY A1107 "
           pdb=" N   ASP A1108 "
           pdb=" CA  ASP A1108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 726
       0.030 -    0.060: 450
       0.060 -    0.090: 84
       0.090 -    0.120: 54
       0.120 -    0.150: 16
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CA  ASN A1066 "
            pdb=" N   ASN A1066 "
            pdb=" C   ASN A1066 "
            pdb=" CB  ASN A1066 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  ASN B1066 "
            pdb=" N   ASN B1066 "
            pdb=" C   ASN B1066 "
            pdb=" CB  ASN B1066 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  MET B 947 "
            pdb=" N   MET B 947 "
            pdb=" C   MET B 947 "
            pdb=" CB  MET B 947 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 693 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 694 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 694 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 694 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 693 "    0.041 5.00e-02 4.00e+02   6.29e-02 6.33e+00
        pdb=" N   PRO B 694 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 694 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 694 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 705 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO B 706 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 706 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 706 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 2304
        2.82 -     3.34: 7636
        3.34 -     3.86: 12166
        3.86 -     4.38: 13877
        4.38 -     4.90: 25290
  Nonbonded interactions: 61273
  Sorted by model distance:
  nonbonded pdb=" N   GLY A 684 "
            pdb=" OE2 GLU A 811 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" NE2 GLN B1089 "
            pdb=" OG1 THR B1092 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" N   GLY B 684 "
            pdb=" OE2 GLU B 811 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   ALA B1074 "
            pdb=" N   ALA B1076 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   GLY A 758 "
            pdb=" NH2 ARG A1090 "
     model   vdw
     2.432 3.120
  ... (remaining 61268 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:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.360
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.005   0.046   8272  Z= 0.206
  Angle     :  0.637   8.332  11226  Z= 0.340
  Chirality :  0.042   0.150   1330
  Planarity :  0.005   0.063   1378
  Dihedral  : 14.001  89.730   2990
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.94 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.77 %
  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:  0.79 (0.26), residues: 1014
  helix:  1.41 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.00 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.007   0.001   HIS A1149 
 PHE   0.009   0.002   PHE A1166 
 TYR   0.011   0.002   TYR B1124 
 ARG   0.002   0.000   ARG A 933 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15890 (  456)
  hydrogen bonds       : angle       4.52948 ( 1341)
  covalent geometry    : bond        0.00509 ( 8272)
  covalent geometry    : angle       0.63665 (11226)

*********************** 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
  145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.7135 (m-30) cc_final: 0.6919 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 145
  average time/residue: 0.2420
  time to fit residues: 45.1345
Evaluate side-chains
  132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1089 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 785 ASN
A1027 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.102530 restraints weight = 8624.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.79
r_work: 0.2895 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.0841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8272  Z= 0.126
  Angle     :  0.531   8.753  11226  Z= 0.271
  Chirality :  0.039   0.139   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  4.299  49.426   1099
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.85 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  5.81 %
    Favored  : 92.71 %
  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:  1.29 (0.27), residues: 1014
  helix:  1.81 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.004   0.001   HIS A1149 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.003   0.000   ARG B 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05651 (  456)
  hydrogen bonds       : angle       3.66454 ( 1341)
  covalent geometry    : bond        0.00279 ( 8272)
  covalent geometry    : angle       0.53131 (11226)

*********************** 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
  150 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7243 (mp)
REVERT: B  688 ASP cc_start: 0.6481 (m-30) cc_final: 0.6260 (m-30)
REVERT: B  738 ILE cc_start: 0.8246 (mt) cc_final: 0.8023 (mt)
REVERT: B  805 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7337 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 141
  average time/residue: 0.2270
  time to fit residues: 41.8749
Evaluate side-chains
  140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain B residue  805 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 61 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.143434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.103828 restraints weight = 8736.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.84
r_work: 0.2912 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   8272  Z= 0.114
  Angle     :  0.494   8.736  11226  Z= 0.252
  Chirality :  0.038   0.131   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.631  17.902   1096
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.94 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.86 %
    Favored  : 91.12 %
  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:  1.48 (0.27), residues: 1014
  helix:  1.99 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.006   0.001   HIS A 786 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.008   0.001   TYR B1124 
 ARG   0.006   0.000   ARG B 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04960 (  456)
  hydrogen bonds       : angle       3.53334 ( 1341)
  covalent geometry    : bond        0.00252 ( 8272)
  covalent geometry    : angle       0.49430 (11226)

*********************** 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
  140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6494 (m-30) cc_final: 0.6290 (m-30)
REVERT: A  805 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7270 (mp)
REVERT: B  688 ASP cc_start: 0.6630 (m-30) cc_final: 0.6402 (m-30)
REVERT: B  805 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7331 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 135
  average time/residue: 0.2443
  time to fit residues: 43.4823
Evaluate side-chains
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0020
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7788

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.146435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.107449 restraints weight = 8682.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.82
r_work: 0.2914 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   8272  Z= 0.122
  Angle     :  0.492   8.639  11226  Z= 0.250
  Chirality :  0.038   0.137   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.580  17.600   1096
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.45 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.34 %
    Favored  : 89.29 %
  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:  1.54 (0.27), residues: 1014
  helix:  2.04 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.00 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 795 
 HIS   0.004   0.001   HIS A1149 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.009   0.001   TYR B1124 
 ARG   0.004   0.000   ARG B 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05056 (  456)
  hydrogen bonds       : angle       3.48666 ( 1341)
  covalent geometry    : bond        0.00286 ( 8272)
  covalent geometry    : angle       0.49236 (11226)

*********************** 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
  143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6592 (m-30) cc_final: 0.6325 (m-30)
REVERT: A  805 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7296 (mp)
REVERT: B  688 ASP cc_start: 0.6740 (m-30) cc_final: 0.6508 (m-30)
REVERT: B  805 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7298 (mp)
REVERT: B  818 PHE cc_start: 0.8761 (m-10) cc_final: 0.8508 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 137
  average time/residue: 0.2285
  time to fit residues: 41.0681
Evaluate side-chains
  141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  947 MET
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  947 MET
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1023 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.141696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.102338 restraints weight = 8656.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.83
r_work: 0.2902 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8272  Z= 0.132
  Angle     :  0.502   8.571  11226  Z= 0.255
  Chirality :  0.039   0.140   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.584  16.869   1096
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.55 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.36 %
    Favored  : 88.15 %
  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:  1.54 (0.27), residues: 1014
  helix:  2.03 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.99 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.004   0.001   HIS A1149 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.010   0.001   TYR A1124 
 ARG   0.002   0.000   ARG A1090 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05286 (  456)
  hydrogen bonds       : angle       3.48979 ( 1341)
  covalent geometry    : bond        0.00316 ( 8272)
  covalent geometry    : angle       0.50188 (11226)

*********************** 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
  146 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6555 (m-30) cc_final: 0.6322 (m-30)
REVERT: A  805 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7283 (mp)
REVERT: B  688 ASP cc_start: 0.6720 (m-30) cc_final: 0.6479 (m-30)
REVERT: B  805 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7284 (mp)
REVERT: B  818 PHE cc_start: 0.8761 (m-10) cc_final: 0.8506 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 138
  average time/residue: 0.2351
  time to fit residues: 42.5694
Evaluate side-chains
  140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue  970 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.144054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.104710 restraints weight = 8643.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.86
r_work: 0.2929 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8272  Z= 0.103
  Angle     :  0.471   8.529  11226  Z= 0.239
  Chirality :  0.037   0.137   1330
  Planarity :  0.005   0.067   1378
  Dihedral  :  3.459  15.602   1096
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.35 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.93 %
    Favored  : 87.81 %
  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:  1.68 (0.27), residues: 1014
  helix:  2.15 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.93 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.002   0.001   HIS B 850 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.008   0.001   TYR A1124 
 ARG   0.002   0.000   ARG B1211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  456)
  hydrogen bonds       : angle       3.43480 ( 1341)
  covalent geometry    : bond        0.00228 ( 8272)
  covalent geometry    : angle       0.47093 (11226)

*********************** 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
  148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6782 (m-30) cc_final: 0.6466 (m-30)
REVERT: A  805 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7356 (mp)
REVERT: B  688 ASP cc_start: 0.6771 (m-30) cc_final: 0.6487 (m-30)
REVERT: B  805 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7362 (mp)
REVERT: B  818 PHE cc_start: 0.8781 (m-10) cc_final: 0.8524 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 143
  average time/residue: 0.2308
  time to fit residues: 43.3269
Evaluate side-chains
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.147601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.109123 restraints weight = 8615.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.78
r_work: 0.2912 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8272  Z= 0.130
  Angle     :  0.495   8.453  11226  Z= 0.252
  Chirality :  0.039   0.148   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.505  15.819   1096
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.85 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.62 %
    Favored  : 87.13 %
  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:  1.62 (0.27), residues: 1014
  helix:  2.11 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.94 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A1149 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.002   0.000   ARG A1090 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05063 (  456)
  hydrogen bonds       : angle       3.45159 ( 1341)
  covalent geometry    : bond        0.00313 ( 8272)
  covalent geometry    : angle       0.49500 (11226)

*********************** 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
  142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6728 (m-30) cc_final: 0.6409 (m-30)
REVERT: A  805 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7269 (mp)
REVERT: B  688 ASP cc_start: 0.6711 (m-30) cc_final: 0.6423 (m-30)
REVERT: B  805 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7293 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 135
  average time/residue: 0.2391
  time to fit residues: 42.5073
Evaluate side-chains
  141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  947 MET
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0870
   chunk 100 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0670
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.5900

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.143781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.103994 restraints weight = 8741.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.98
r_work: 0.2915 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8272  Z= 0.108
  Angle     :  0.473   8.407  11226  Z= 0.240
  Chirality :  0.038   0.138   1330
  Planarity :  0.005   0.067   1378
  Dihedral  :  3.420  14.670   1096
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.55 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.85 %
    Favored  : 87.02 %
  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:  1.70 (0.27), residues: 1014
  helix:  2.16 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.89 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.002   0.001   HIS B 850 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.008   0.001   TYR A1124 
 ARG   0.002   0.000   ARG B 690 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  456)
  hydrogen bonds       : angle       3.42927 ( 1341)
  covalent geometry    : bond        0.00246 ( 8272)
  covalent geometry    : angle       0.47256 (11226)

*********************** 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
  139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6595 (m-30) cc_final: 0.6330 (m-30)
REVERT: A  690 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7733 (mtp85)
REVERT: A  805 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7189 (mp)
REVERT: B  688 ASP cc_start: 0.6598 (m-30) cc_final: 0.6298 (m-30)
REVERT: B  805 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7180 (mp)
REVERT: B  818 PHE cc_start: 0.8676 (m-10) cc_final: 0.8420 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 133
  average time/residue: 0.2386
  time to fit residues: 41.8874
Evaluate side-chains
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  947 MET
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    0.0980
   chunk 101 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 63 optimal weight:    0.4980
   chunk 80 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.142308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102257 restraints weight = 8739.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.04
r_work: 0.2883 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8272  Z= 0.125
  Angle     :  0.492   8.301  11226  Z= 0.250
  Chirality :  0.038   0.155   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.456  14.867   1096
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.55 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.73 %
    Favored  : 87.02 %
  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:  1.74 (0.27), residues: 1014
  helix:  2.26 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.93 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.003   0.001   HIS B 850 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.010   0.001   TYR A1124 
 ARG   0.004   0.000   ARG B1211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04977 (  456)
  hydrogen bonds       : angle       3.44356 ( 1341)
  covalent geometry    : bond        0.00297 ( 8272)
  covalent geometry    : angle       0.49217 (11226)

*********************** 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
  140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6678 (m-30) cc_final: 0.6409 (m-30)
REVERT: A  805 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7296 (mp)
REVERT: B  688 ASP cc_start: 0.6638 (m-30) cc_final: 0.6345 (m-30)
REVERT: B  805 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7248 (mp)
REVERT: B  818 PHE cc_start: 0.8697 (m-10) cc_final: 0.8447 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 133
  average time/residue: 0.2443
  time to fit residues: 42.9720
Evaluate side-chains
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0010
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7386

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.142908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.102720 restraints weight = 8593.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.97
r_work: 0.2895 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8272  Z= 0.118
  Angle     :  0.488   8.217  11226  Z= 0.248
  Chirality :  0.038   0.147   1330
  Planarity :  0.005   0.067   1378
  Dihedral  :  3.432  14.300   1096
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.35 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.85 %
    Favored  : 86.90 %
  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:  1.75 (0.27), residues: 1014
  helix:  2.27 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.91 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A1149 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.009   0.001   TYR A1124 
 ARG   0.004   0.000   ARG B1211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  456)
  hydrogen bonds       : angle       3.44995 ( 1341)
  covalent geometry    : bond        0.00279 ( 8272)
  covalent geometry    : angle       0.48805 (11226)

********************** 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
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A  688 ASP cc_start: 0.6670 (m-30) cc_final: 0.6415 (m-30)
REVERT: A  690 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7928 (mtt-85)
REVERT: A  805 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7299 (mp)
REVERT: B  688 ASP cc_start: 0.6674 (m-30) cc_final: 0.6383 (m-30)
REVERT: B  805 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7299 (mp)
REVERT: B  818 PHE cc_start: 0.8704 (m-10) cc_final: 0.8452 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 132
  average time/residue: 0.2322
  time to fit residues: 40.3586
Evaluate side-chains
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 99 optimal weight:    0.3980
   chunk 95 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 101 optimal weight:    0.3980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.143381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.103224 restraints weight = 8646.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.98
r_work: 0.2901 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8272  Z= 0.113
  Angle     :  0.483   8.090  11226  Z= 0.246
  Chirality :  0.038   0.148   1330
  Planarity :  0.005   0.067   1378
  Dihedral  :  3.381  14.262   1096
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.55 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.96 %
    Favored  : 86.56 %
  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:  1.80 (0.27), residues: 1014
  helix:  2.31 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.89 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.009   0.001   TYR A1124 
 ARG   0.004   0.000   ARG B1211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 (  456)
  hydrogen bonds       : angle       3.43022 ( 1341)
  covalent geometry    : bond        0.00260 ( 8272)
  covalent geometry    : angle       0.48348 (11226)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4576.62 seconds
wall clock time: 79 minutes 31.07 seconds (4771.07 seconds total)