Starting phenix.real_space_refine
on Mon Mar 11 10:57:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/03_2024/8gvc_34290_trim_updated.pdb"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.165
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5372      2.51       5
     N    1326      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  736": "OD1" <-> "OD2"
    Residue "A PHE  847": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  937": "OD1" <-> "OD2"
    Residue "A PHE  989": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1151": "OD1" <-> "OD2"
    Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  699": "OD1" <-> "OD2"
    Residue "B PHE  847": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  937": "OD1" <-> "OD2"
    Residue "B GLU  955": "OE1" <-> "OE2"
    Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 8080
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.81, per 1000 atoms: 0.72
  Number of scatterers: 8080
  At special positions: 0
  Unit cell: (89.1, 129.8, 81.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1336      8.00
     N    1326      7.00
     C    5372      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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: 3.80
  Conformation dependent library (CDL) restraints added in 1.6 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...
  running ksdssp...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      66.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 683 through 695
      Proline residue:  A 694  - end of helix
    Processing helix  chain 'A' and resid 697 through 703
      removed outlier: 4.271A  pdb=" N   ALA A 703 " --> pdb=" O   ASP A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 733
      removed outlier: 4.070A  pdb=" N   PHE A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA A 718 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 741 through 757
    Processing helix  chain 'A' and resid 769 through 785
      removed outlier: 3.781A  pdb=" N   ASN A 785 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 809
      removed outlier: 3.938A  pdb=" N   ILE A 796 " --> pdb=" O   GLY A 792 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY A 797 " --> pdb=" O   ARG A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 818
      removed outlier: 3.838A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 849
      removed outlier: 4.107A  pdb=" N   ILE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 845 " --> pdb=" O   TYR A 841 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A 846 " --> pdb=" O   LYS A 842 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 923
      removed outlier: 3.646A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 953
      removed outlier: 3.583A  pdb=" N   PHE A 938 " --> pdb=" O   VAL A 934 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY A 939 " --> pdb=" O   ILE A 935 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   VAL A 940 " --> pdb=" O   GLY A 936 " (cutoff:3.500A)
      Proline residue:  A 941  - end of helix
    Processing helix  chain 'A' and resid 973 through 975
      No H-bonds generated for 'chain 'A' and resid 973 through 975'
    Processing helix  chain 'A' and resid 991 through 1020
      removed outlier: 3.713A  pdb=" N   VAL A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   LEU A 998 " --> pdb=" O   MET A 994 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU A 999 " --> pdb=" O   VAL A 995 " (cutoff:3.500A)
      Proline residue:  A1000  - end of helix
    Processing helix  chain 'A' and resid 1034 through 1049
      removed outlier: 3.570A  pdb=" N   ALA A1047 " --> pdb=" O   GLY A1043 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   LEU A1048 " --> pdb=" O   GLY A1044 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   PHE A1049 " --> pdb=" O   ILE A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1065
    Processing helix  chain 'A' and resid 1092 through 1101
    Processing helix  chain 'A' and resid 1110 through 1112
      No H-bonds generated for 'chain 'A' and resid 1110 through 1112'
    Processing helix  chain 'A' and resid 1115 through 1130
      removed outlier: 3.525A  pdb=" N   ILE A1121 " --> pdb=" O   VAL A1117 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A1130 " --> pdb=" O   GLY A1126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1142
      removed outlier: 3.660A  pdb=" N   HIS A1140 " --> pdb=" O   TYR A1136 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A1141 " --> pdb=" O   GLU A1137 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU A1142 " --> pdb=" O   ARG A1138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1148
      No H-bonds generated for 'chain 'A' and resid 1146 through 1148'
    Processing helix  chain 'A' and resid 1153 through 1156
      No H-bonds generated for 'chain 'A' and resid 1153 through 1156'
    Processing helix  chain 'A' and resid 1160 through 1182
    Processing helix  chain 'A' and resid 1186 through 1207
      removed outlier: 3.696A  pdb=" N   PHE A1189 " --> pdb=" O   SER A1186 " (cutoff:3.500A)
      Proline residue:  A1190  - end of helix
      Proline residue:  A1198  - end of helix
      removed outlier: 4.628A  pdb=" N   VAL A1203 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   LEU A1204 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR A1205 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1216
    Processing helix  chain 'B' and resid 683 through 695
      Proline residue:  B 694  - end of helix
    Processing helix  chain 'B' and resid 697 through 703
      removed outlier: 4.350A  pdb=" N   ALA B 703 " --> pdb=" O   ASP B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 733
      removed outlier: 4.067A  pdb=" N   PHE B 717 " --> pdb=" O   ILE B 713 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 718 " --> pdb=" O   PHE B 714 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
    Processing helix  chain 'B' and resid 741 through 757
    Processing helix  chain 'B' and resid 769 through 785
    Processing helix  chain 'B' and resid 789 through 809
      removed outlier: 3.998A  pdb=" N   ARG B 793 " --> pdb=" O   TYR B 789 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 818
      removed outlier: 3.912A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 849
      removed outlier: 4.099A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU B 843 " --> pdb=" O   THR B 839 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 844 " --> pdb=" O   PHE B 840 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS B 845 " --> pdb=" O   TYR B 841 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE B 846 " --> pdb=" O   LYS B 842 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 901 through 923
      removed outlier: 3.517A  pdb=" N   LEU B 905 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 953
      removed outlier: 3.530A  pdb=" N   PHE B 938 " --> pdb=" O   VAL B 934 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY B 939 " --> pdb=" O   ILE B 935 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   VAL B 940 " --> pdb=" O   GLY B 936 " (cutoff:3.500A)
      Proline residue:  B 941  - end of helix
    Processing helix  chain 'B' and resid 973 through 975
      No H-bonds generated for 'chain 'B' and resid 973 through 975'
    Processing helix  chain 'B' and resid 992 through 1020
      removed outlier: 5.491A  pdb=" N   LEU B 998 " --> pdb=" O   MET B 994 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   LEU B 999 " --> pdb=" O   VAL B 995 " (cutoff:3.500A)
      Proline residue:  B1000  - end of helix
    Processing helix  chain 'B' and resid 1034 through 1049
      removed outlier: 3.534A  pdb=" N   ALA B1047 " --> pdb=" O   GLY B1043 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU B1048 " --> pdb=" O   GLY B1044 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   PHE B1049 " --> pdb=" O   ILE B1045 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1059 through 1065
    Processing helix  chain 'B' and resid 1092 through 1101
    Processing helix  chain 'B' and resid 1110 through 1112
      No H-bonds generated for 'chain 'B' and resid 1110 through 1112'
    Processing helix  chain 'B' and resid 1115 through 1130
      removed outlier: 3.524A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU B1130 " --> pdb=" O   GLY B1126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1134 through 1142
      removed outlier: 3.726A  pdb=" N   LEU B1141 " --> pdb=" O   GLU B1137 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B1142 " --> pdb=" O   ARG B1138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1146 through 1148
      No H-bonds generated for 'chain 'B' and resid 1146 through 1148'
    Processing helix  chain 'B' and resid 1153 through 1156
      No H-bonds generated for 'chain 'B' and resid 1153 through 1156'
    Processing helix  chain 'B' and resid 1160 through 1182
    Processing helix  chain 'B' and resid 1186 through 1207
      removed outlier: 3.681A  pdb=" N   PHE B1189 " --> pdb=" O   SER B1186 " (cutoff:3.500A)
      Proline residue:  B1190  - end of helix
      Proline residue:  B1198  - end of helix
      removed outlier: 4.594A  pdb=" N   VAL B1203 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   LEU B1204 " --> pdb=" O   MET B1201 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR B1205 " --> pdb=" O   VAL B1202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1216

    403 hydrogen bonds defined for protein.
    1143 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: 2.00

  Time building geometry restraints manager: 4.12 seconds

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

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

  Histogram of bond angle deviations from ideal:
      100.59 -   107.27: 311
      107.27 -   113.94: 4779
      113.94 -   120.62: 3420
      120.62 -   127.29: 2631
      127.29 -   133.97: 91
  Bond angle restraints: 11232
  Sorted by residual:
  angle pdb=" N   VAL B 948 "
        pdb=" CA  VAL B 948 "
        pdb=" C   VAL B 948 "
      ideal   model   delta    sigma   weight residual
     110.72  104.86    5.86 1.01e+00 9.80e-01 3.36e+01
  angle pdb=" N   VAL A 948 "
        pdb=" CA  VAL A 948 "
        pdb=" C   VAL A 948 "
      ideal   model   delta    sigma   weight residual
     110.72  104.87    5.85 1.01e+00 9.80e-01 3.36e+01
  angle pdb=" N   ILE A 946 "
        pdb=" CA  ILE A 946 "
        pdb=" C   ILE A 946 "
      ideal   model   delta    sigma   weight residual
     110.42  114.55   -4.13 9.60e-01 1.09e+00 1.85e+01
  angle pdb=" N   ILE B 946 "
        pdb=" CA  ILE B 946 "
        pdb=" C   ILE B 946 "
      ideal   model   delta    sigma   weight residual
     110.42  114.52   -4.10 9.60e-01 1.09e+00 1.82e+01
  angle pdb=" O1  BCT B1301 "
        pdb=" C   BCT B1301 "
        pdb=" O2  BCT B1301 "
      ideal   model   delta    sigma   weight residual
     129.92  117.82   12.10 3.00e+00 1.11e-01 1.63e+01
  ... (remaining 11227 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        1.67 -     2.32: 10
        2.32 -     2.96: 3988
        2.96 -     3.61: 11290
        3.61 -     4.25: 17063
        4.25 -     4.90: 30000
  Nonbonded interactions: 62351
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 820 "
            pdb=" CZ  ARG A1200 "
     model   vdw
     1.670 3.270
  nonbonded pdb=" OG  SER A 820 "
            pdb=" NE  ARG A1200 "
     model   vdw
     1.925 2.520
  nonbonded pdb=" O   ALA B1057 "
            pdb=" OG1 THR B1058 "
     model   vdw
     2.031 2.440
  nonbonded pdb=" O   ASP A 956 "
            pdb=" OD1 ASP A 956 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OD1 ASP A1151 "
            pdb=" NZ  LYS A1156 "
     model   vdw
     2.148 2.520
  ... (remaining 62346 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:             0.940
  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:          4.340
  Check model and map are aligned:         0.120
  Set scattering table:                    0.090
  Process input model:                     27.560
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.078   8278  Z= 0.160
  Angle     :  0.481  12.101  11232  Z= 0.267
  Chirality :  0.036   0.193   1330
  Planarity :  0.003   0.041   1380
  Dihedral  : 14.663  80.557   2990
  Min Nonbonded Distance : 1.670

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.97 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.10 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.28), residues: 1014
  helix:  2.37 (0.22), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 362

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

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6906 (mtp180)
REVERT: A 1163 MET cc_start: 0.7431 (ttp) cc_final: 0.6840 (ttp)
REVERT: B 1205 THR cc_start: 0.8454 (m) cc_final: 0.8070 (p)
REVERT: B 1206 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6710 (ttp-170)
  outliers start: 10
  outliers final: 9
  residues processed: 132
  average time/residue: 1.2850
  time to fit residues: 179.2585
Evaluate side-chains
  125 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1209 THR
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1183 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.0779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8278  Z= 0.189
  Angle     :  0.509   8.914  11232  Z= 0.255
  Chirality :  0.038   0.136   1330
  Planarity :  0.004   0.053   1380
  Dihedral  :  3.801  23.165   1105
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.66 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.55 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.28), residues: 1014
  helix:  2.31 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.54 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.011   0.001   PHE B 774 
 TYR   0.009   0.001   TYR B1124 
 ARG   0.006   0.000   ARG B1206 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6883 (mtp180)
REVERT: B 1163 MET cc_start: 0.7556 (ttp) cc_final: 0.6948 (ttp)
REVERT: B 1206 ARG cc_start: 0.7376 (mtm110) cc_final: 0.6841 (ttp-170)
  outliers start: 16
  outliers final: 8
  residues processed: 124
  average time/residue: 1.3410
  time to fit residues: 176.0174
Evaluate side-chains
  119 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.3186

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8278  Z= 0.265
  Angle     :  0.547   8.744  11232  Z= 0.277
  Chirality :  0.040   0.149   1330
  Planarity :  0.005   0.055   1380
  Dihedral  :  3.669  21.139   1097
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.56 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.58 %
    Favored  : 83.60 %
  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:  1.65 (0.28), residues: 1014
  helix:  2.10 (0.22), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.70 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.004   0.001   HIS A1149 
 PHE   0.010   0.001   PHE B 774 
 TYR   0.014   0.002   TYR B1124 
 ARG   0.006   0.000   ARG B 933 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A  701 ARG cc_start: 0.7015 (mtt-85) cc_final: 0.6773 (mtt-85)
REVERT: B 1071 MET cc_start: 0.8262 (mmm) cc_final: 0.7953 (mmt)
REVERT: B 1163 MET cc_start: 0.7726 (ttp) cc_final: 0.7140 (ttp)
REVERT: B 1206 ARG cc_start: 0.7390 (mtm110) cc_final: 0.6794 (ttp-170)
  outliers start: 16
  outliers final: 12
  residues processed: 119
  average time/residue: 1.4043
  time to fit residues: 176.2474
Evaluate side-chains
  124 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  994 MET
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8278  Z= 0.213
  Angle     :  0.510   8.709  11232  Z= 0.257
  Chirality :  0.039   0.140   1330
  Planarity :  0.005   0.054   1380
  Dihedral  :  3.632  19.500   1097
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.37 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.49 %
    Favored  : 82.69 %
  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:  2.07 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.69 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.011   0.001   TYR B1124 
 ARG   0.006   0.000   ARG B 933 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6856 (mtp180)
REVERT: A  701 ARG cc_start: 0.7007 (mtt-85) cc_final: 0.6790 (mtt-85)
REVERT: B  687 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6766 (mtp180)
REVERT: B  736 ASP cc_start: 0.7316 (t0) cc_final: 0.7082 (t0)
REVERT: B 1163 MET cc_start: 0.7603 (ttp) cc_final: 0.6968 (ttp)
REVERT: B 1206 ARG cc_start: 0.7420 (mtm110) cc_final: 0.6859 (ttp-170)
  outliers start: 16
  outliers final: 11
  residues processed: 128
  average time/residue: 1.2891
  time to fit residues: 174.4020
Evaluate side-chains
  124 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1205 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:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8278  Z= 0.294
  Angle     :  0.563   8.650  11232  Z= 0.284
  Chirality :  0.040   0.156   1330
  Planarity :  0.005   0.056   1380
  Dihedral  :  3.800  20.074   1097
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.86 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.83 %
    Favored  : 81.55 %
  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:  1.47 (0.27), residues: 1014
  helix:  1.98 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.80 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.010   0.001   PHE A 835 
 TYR   0.015   0.001   TYR B1124 
 ARG   0.006   0.001   ARG B 933 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7191 (mtm110) cc_final: 0.6898 (mtp180)
REVERT: A  689 VAL cc_start: 0.7915 (t) cc_final: 0.7686 (t)
REVERT: B  689 VAL cc_start: 0.7878 (t) cc_final: 0.7656 (t)
REVERT: B  736 ASP cc_start: 0.7396 (t0) cc_final: 0.7155 (t0)
REVERT: B 1163 MET cc_start: 0.7733 (ttp) cc_final: 0.7214 (ttp)
REVERT: B 1206 ARG cc_start: 0.7424 (mtm110) cc_final: 0.6845 (ttp-170)
  outliers start: 23
  outliers final: 16
  residues processed: 131
  average time/residue: 1.3000
  time to fit residues: 180.1514
Evaluate side-chains
  126 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  895 ARG
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8278  Z= 0.230
  Angle     :  0.526   8.687  11232  Z= 0.265
  Chirality :  0.039   0.146   1330
  Planarity :  0.005   0.055   1380
  Dihedral  :  3.730  18.875   1097
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.47 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.40 %
    Favored  : 81.21 %
  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:  2.01 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -0.82 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.009   0.001   PHE B 774 
 TYR   0.011   0.001   TYR B1124 
 ARG   0.007   0.001   ARG B 687 

*********************** 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
  130 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7182 (mtm110) cc_final: 0.6873 (mtp180)
REVERT: A  689 VAL cc_start: 0.7876 (t) cc_final: 0.7654 (t)
REVERT: A 1163 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7125 (ttt)
REVERT: B  687 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6955 (mtp180)
REVERT: B  689 VAL cc_start: 0.7845 (t) cc_final: 0.7628 (t)
REVERT: B 1163 MET cc_start: 0.7631 (ttp) cc_final: 0.7051 (ttp)
REVERT: B 1206 ARG cc_start: 0.7440 (mtm110) cc_final: 0.6910 (ttp-170)
  outliers start: 21
  outliers final: 17
  residues processed: 119
  average time/residue: 1.3675
  time to fit residues: 171.7993
Evaluate side-chains
  126 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1183 THR
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  895 ARG
Chi-restraints excluded: chain B residue 1104 ILE
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1205 THR
Chi-restraints excluded: chain B residue 1209 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0970
   chunk 60 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0570
   chunk 58 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8278  Z= 0.143
  Angle     :  0.465   8.646  11232  Z= 0.234
  Chirality :  0.037   0.128   1330
  Planarity :  0.004   0.055   1380
  Dihedral  :  3.469  16.843   1097
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.47 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.31 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.27), residues: 1014
  helix:  2.25 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.74 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 795 
 HIS   0.003   0.001   HIS B 850 
 PHE   0.008   0.001   PHE B 774 
 TYR   0.006   0.001   TYR B1124 
 ARG   0.007   0.000   ARG B 933 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A  689 VAL cc_start: 0.7871 (t) cc_final: 0.7640 (t)
REVERT: B  689 VAL cc_start: 0.7775 (t) cc_final: 0.7569 (t)
REVERT: B  736 ASP cc_start: 0.7275 (t0) cc_final: 0.7045 (t0)
REVERT: B  805 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7824 (mt)
REVERT: B 1027 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6966 (mp10)
REVERT: B 1206 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6920 (ttp-170)
  outliers start: 12
  outliers final: 7
  residues processed: 130
  average time/residue: 1.2931
  time to fit residues: 177.5426
Evaluate side-chains
  123 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  895 ARG
Chi-restraints excluded: chain B residue 1027 GLN
Chi-restraints excluded: chain B residue 1109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0570
   chunk 89 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8278  Z= 0.157
  Angle     :  0.490   8.683  11232  Z= 0.243
  Chirality :  0.037   0.131   1330
  Planarity :  0.004   0.056   1380
  Dihedral  :  3.383  16.413   1096
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.47 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.45 %
    Favored  : 80.30 %
  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:  1.81 (0.27), residues: 1014
  helix:  2.30 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.71 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 795 
 HIS   0.005   0.001   HIS B 850 
 PHE   0.008   0.001   PHE A 938 
 TYR   0.009   0.001   TYR A1124 
 ARG   0.008   0.000   ARG B 687 

*********************** 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
  124 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6929 (mtp180)
REVERT: A  689 VAL cc_start: 0.7871 (t) cc_final: 0.7647 (t)
REVERT: B  687 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6998 (mtm110)
REVERT: B  689 VAL cc_start: 0.7772 (t) cc_final: 0.7566 (t)
REVERT: B  805 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7855 (mt)
REVERT: B 1027 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7008 (mp10)
REVERT: B 1206 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6920 (ttp-170)
  outliers start: 11
  outliers final: 4
  residues processed: 119
  average time/residue: 1.3364
  time to fit residues: 168.1094
Evaluate side-chains
  117 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1027 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0870
   chunk 82 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8278  Z= 0.150
  Angle     :  0.485   8.637  11232  Z= 0.239
  Chirality :  0.037   0.131   1330
  Planarity :  0.004   0.057   1380
  Dihedral  :  3.324  16.110   1096
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.37 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 18.79 %
    Favored  : 80.18 %
  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:  1.85 (0.27), residues: 1014
  helix:  2.32 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.68 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.007   0.001   PHE A 938 
 TYR   0.008   0.001   TYR B1124 
 ARG   0.007   0.000   ARG B 933 

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

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6913 (mtm110)
REVERT: A  689 VAL cc_start: 0.7797 (t) cc_final: 0.7571 (t)
REVERT: B  687 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6992 (mtm110)
REVERT: B  736 ASP cc_start: 0.7265 (t0) cc_final: 0.7019 (t0)
REVERT: B  805 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (mt)
REVERT: B  895 ARG cc_start: 0.7075 (mpt-90) cc_final: 0.6824 (ttm110)
REVERT: B 1022 LYS cc_start: 0.6793 (mmmt) cc_final: 0.6391 (mmtp)
REVERT: B 1027 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.6946 (mp10)
REVERT: B 1088 GLU cc_start: 0.7586 (pm20) cc_final: 0.7220 (mp0)
REVERT: B 1206 ARG cc_start: 0.7411 (mtm110) cc_final: 0.6924 (ttp-170)
  outliers start: 9
  outliers final: 6
  residues processed: 123
  average time/residue: 1.3819
  time to fit residues: 179.3447
Evaluate side-chains
  124 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1104 ILE
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1027 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 93 optimal weight:    0.2980
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8278  Z= 0.188
  Angle     :  0.510   8.615  11232  Z= 0.252
  Chirality :  0.038   0.143   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.405  16.195   1096
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.56 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.79 %
    Favored  : 79.95 %
  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:  1.74 (0.27), residues: 1014
  helix:  2.19 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.70 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 795 
 HIS   0.005   0.001   HIS A 850 
 PHE   0.008   0.001   PHE B 774 
 TYR   0.011   0.001   TYR B1124 
 ARG   0.007   0.000   ARG B 933 

********************** 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
  117 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  687 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6932 (mtm110)
REVERT: A  689 VAL cc_start: 0.7830 (t) cc_final: 0.7629 (t)
REVERT: A 1007 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7055 (mt)
REVERT: B  687 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6944 (mtm110)
REVERT: B  805 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7864 (mt)
REVERT: B 1027 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6961 (mp10)
REVERT: B 1163 MET cc_start: 0.7486 (ttp) cc_final: 0.6861 (ttp)
REVERT: B 1206 ARG cc_start: 0.7413 (mtm110) cc_final: 0.6877 (ttp-170)
  outliers start: 11
  outliers final: 5
  residues processed: 113
  average time/residue: 1.4767
  time to fit residues: 175.6477
Evaluate side-chains
  114 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue 1027 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.0470
   chunk 81 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.0880

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

Flipped N/Q/H residues before XYZ refinement:
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.152507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.109368 restraints weight = 8330.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.02
r_work: 0.3258 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8278  Z= 0.230
  Angle     :  0.542   9.252  11232  Z= 0.268
  Chirality :  0.039   0.152   1330
  Planarity :  0.005   0.057   1380
  Dihedral  :  3.543  15.909   1096
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.06 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 18.56 %
    Favored  : 80.07 %
  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:  1.66 (0.27), residues: 1014
  helix:  2.12 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.69 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.010   0.001   PHE B 835 
 TYR   0.012   0.001   TYR A1124 
 ARG   0.007   0.000   ARG A 933 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3316.68 seconds
wall clock time: 59 minutes 37.45 seconds (3577.45 seconds total)