Starting phenix.real_space_refine
on Tue Feb 13 23:25:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_34292.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_34292.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_34292.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_34292.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvf_34292/02_2024/8gvf_34292.pdb"
  }
  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
    Residue "B PHE  847": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.55, per 1000 atoms: 0.56
  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  - 3.50
        Amino acid           : False - 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: 3.01
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 696 through 702
      removed outlier: 3.536A  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: 2.08

  Time building geometry restraints manager: 3.29 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:
       97.70 -   104.96: 171
      104.96 -   112.23: 4252
      112.23 -   119.49: 2739
      119.49 -   126.75: 3950
      126.75 -   134.02: 114
  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 2.520
  nonbonded pdb=" NE2 GLN B1089 "
            pdb=" OG1 THR B1092 "
     model   vdw
     2.314 2.520
  nonbonded pdb=" N   GLY B 684 "
            pdb=" OE2 GLU B 811 "
     model   vdw
     2.328 2.520
  nonbonded pdb=" O   ALA B1074 "
            pdb=" N   ALA B1076 "
     model   vdw
     2.377 2.520
  nonbonded pdb=" O   GLY A 758 "
            pdb=" NH2 ARG A1090 "
     model   vdw
     2.432 2.520
  ... (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
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:             1.770
  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:          4.980
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     24.430
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.450
-------------------------------------------------------------------------------
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= 0.332
  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 

*********************** 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 fitting.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.819 
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: 0.2467
  time to fit residues: 46.0245
Evaluate side-chains
  132 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 77 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0270
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 785 ASN
A1027 GLN
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.0889

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= 0.161
  Angle     :  0.515   8.611  11226  Z= 0.262
  Chirality :  0.039   0.134   1330
  Planarity :  0.005   0.067   1378
  Dihedral  :  4.074  37.513   1099
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.04 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  5.92 %
    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:  1.31 (0.27), residues: 1014
  helix:  1.84 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.02 (0.31), residues: 354

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

*********************** 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 fitting.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: B  688 ASP cc_start: 0.7023 (m-30) cc_final: 0.6788 (m-30)
REVERT: B  805 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7748 (mp)
  outliers start: 12
  outliers final: 7
  residues processed: 142
  average time/residue: 0.2689
  time to fit residues: 49.6874
Evaluate side-chains
  141 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
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 A residue 1089 GLN
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 51 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0060
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0270
   chunk 82 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8272  Z= 0.156
  Angle     :  0.483   8.619  11226  Z= 0.246
  Chirality :  0.038   0.130   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.905  37.779   1099
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.94 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.97 %
    Favored  : 91.00 %
  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:  1.49 (0.27), residues: 1014
  helix:  2.00 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.02 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.008   0.001   HIS A 786 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.008   0.001   TYR B1124 
 ARG   0.003   0.000   ARG B 690 

*********************** 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
  145 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (mp)
REVERT: B  805 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7729 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 140
  average time/residue: 0.2332
  time to fit residues: 42.7186
Evaluate side-chains
  138 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1089 GLN
Chi-restraints excluded: chain B residue  698 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1089 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.0670
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 93 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8272  Z= 0.210
  Angle     :  0.503   8.564  11226  Z= 0.256
  Chirality :  0.039   0.138   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.865  37.013   1099
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.85 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.00 %
    Favored  : 88.95 %
  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:  2.00 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.03 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.004   0.001   HIS A1149 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.015   0.001   TYR B 952 
 ARG   0.003   0.000   ARG B1090 

*********************** 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
  153 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7727 (mp)
REVERT: B  805 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7705 (mp)
  outliers start: 18
  outliers final: 9
  residues processed: 143
  average time/residue: 0.2371
  time to fit residues: 44.6120
Evaluate side-chains
  147 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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 A residue 1089 GLN
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  956 ASP
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1209 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1185

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= 0.197
  Angle     :  0.495   8.514  11226  Z= 0.251
  Chirality :  0.039   0.141   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.805  35.092   1099
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.65 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.36 %
    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:  1.50 (0.27), residues: 1014
  helix:  2.01 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.01 (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   0.013   0.001   TYR A 952 
 ARG   0.002   0.000   ARG A 690 

*********************** 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
  149 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7710 (mp)
REVERT: B  805 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7715 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 139
  average time/residue: 0.2464
  time to fit residues: 44.5294
Evaluate side-chains
  146 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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 A residue 1089 GLN
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 1089 GLN
Chi-restraints excluded: chain B residue 1209 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   8272  Z= 0.312
  Angle     :  0.560   8.460  11226  Z= 0.285
  Chirality :  0.041   0.153   1330
  Planarity :  0.005   0.070   1378
  Dihedral  :  3.935  32.651   1099
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.75 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.59 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.27), residues: 1014
  helix:  1.96 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.16 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.006   0.001   HIS A1149 
 PHE   0.009   0.001   PHE A 774 
 TYR   0.015   0.002   TYR B 952 
 ARG   0.002   0.000   ARG A1090 

*********************** 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
  155 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A  805 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7773 (mp)
REVERT: B  805 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7738 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 145
  average time/residue: 0.2340
  time to fit residues: 44.4434
Evaluate side-chains
  149 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
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  956 ASP
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1089 GLN
Chi-restraints excluded: chain A residue 1217 ASP
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  956 ASP
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1089 GLN
Chi-restraints excluded: chain B residue 1209 THR
Chi-restraints excluded: chain B residue 1217 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1297

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= 0.162
  Angle     :  0.480   8.549  11226  Z= 0.245
  Chirality :  0.038   0.141   1330
  Planarity :  0.005   0.068   1378
  Dihedral  :  3.746  32.448   1099
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.35 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.30 %
    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:  1.46 (0.27), residues: 1014
  helix:  1.98 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.02 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.009   0.001   TYR B 952 
 ARG   0.003   0.000   ARG B1090 

*********************** 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
  141 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A  805 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7752 (mp)
REVERT: B  805 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7718 (mp)
  outliers start: 10
  outliers final: 6
  residues processed: 136
  average time/residue: 0.2442
  time to fit residues: 43.4939
Evaluate side-chains
  137 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1089 GLN
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0010
   chunk 9 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1335

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= 0.182
  Angle     :  0.488   8.499  11226  Z= 0.248
  Chirality :  0.038   0.145   1330
  Planarity :  0.005   0.069   1378
  Dihedral  :  3.682  31.121   1099
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.55 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.19 %
    Favored  : 86.33 %
  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:  1.55 (0.27), residues: 1014
  helix:  2.12 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.04 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.011   0.001   TYR B 952 
 ARG   0.002   0.000   ARG A 690 

*********************** 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
  145 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  805 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7760 (mp)
REVERT: B  805 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7733 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 137
  average time/residue: 0.2318
  time to fit residues: 41.4222
Evaluate side-chains
  140 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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 A residue 1089 GLN
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 39 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0020
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8590

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1342

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= 0.196
  Angle     :  0.500   8.439  11226  Z= 0.254
  Chirality :  0.039   0.151   1330
  Planarity :  0.005   0.069   1378
  Dihedral  :  3.669  29.566   1099
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.94 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.07 %
    Favored  : 86.22 %
  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:  1.45 (0.27), residues: 1014
  helix:  1.97 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.02 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A1149 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.011   0.001   TYR B 952 
 ARG   0.004   0.000   ARG B1211 

*********************** 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
  147 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A  805 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7767 (mp)
REVERT: B  805 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7723 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2477
  time to fit residues: 46.1044
Evaluate side-chains
  144 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
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 A residue 1089 GLN
Chi-restraints excluded: chain A residue 1209 THR
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
Chi-restraints excluded: chain B residue 1089 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.0670
   chunk 93 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0170
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8272  Z= 0.150
  Angle     :  0.479   8.454  11226  Z= 0.244
  Chirality :  0.038   0.145   1330
  Planarity :  0.005   0.069   1378
  Dihedral  :  3.576  28.668   1099
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.75 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.19 %
    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:  1.61 (0.27), residues: 1014
  helix:  2.16 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.003   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.009   0.001   TYR B 952 
 ARG   0.004   0.000   ARG B1211 

********************** 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
  140 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  805 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: B  805 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 133
  average time/residue: 0.2305
  time to fit residues: 40.3544
Evaluate side-chains
  137 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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 A residue 1089 GLN
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  970 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B1089 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.144152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.103052 restraints weight = 8652.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.11
r_work: 0.2892 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1446

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= 0.167
  Angle     :  0.482   8.385  11226  Z= 0.245
  Chirality :  0.038   0.155   1330
  Planarity :  0.005   0.069   1378
  Dihedral  :  3.548  26.840   1099
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.65 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.53 %
    Favored  : 86.10 %
  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:  2.17 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.99 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.010   0.001   PHE A 774 
 TYR   0.010   0.001   TYR A 952 
 ARG   0.004   0.000   ARG B1211 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2000.11 seconds
wall clock time: 36 minutes 40.34 seconds (2200.34 seconds total)