Starting phenix.real_space_refine
on Mon Mar 11 10:37:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gve_34291/03_2024/8gve_34291.pdb"
  }
  resolution = 3.17
  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=   0.142
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    5359      2.51       5
     N    1323      2.21       5
     O    1326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  682": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  742": "OE1" <-> "OE2"
    Residue "B GLU  849": "OE1" <-> "OE2"
    Residue "B PHE  926": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  937": "OD1" <-> "OD2"
    Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU 1085": "OE1" <-> "OE2"
    Residue "B GLU 1220": "OE1" <-> "OE2"
    Residue "A ASP  673": "OD1" <-> "OD2"
    Residue "A ASP  688": "OD1" <-> "OD2"
    Residue "A ASP  699": "OD1" <-> "OD2"
    Residue "A TYR  716": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  776": "OE1" <-> "OE2"
    Residue "A PHE  818": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  847": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  937": "OD1" <-> "OD2"
    Residue "A ASP  951": "OD1" <-> "OD2"
    Residue "A ASP  956": "OD1" <-> "OD2"
    Residue "A PHE 1049": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1217": "OD1" <-> "OD2"
  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: 8054
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: 4018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4018
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 27, 'TRANS': 481}
          Chain breaks: 1
  Time building chain proxies: 4.65, per 1000 atoms: 0.58
  Number of scatterers: 8054
  At special positions: 0
  Unit cell: (80.3, 73.7, 132, 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    1326      8.00
     N    1323      7.00
     C    5359      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: 3.04
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1900

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 3 sheets defined
      72.1% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'B' and resid 682 through 693
      removed outlier: 3.509A  pdb=" N   TYR B 693 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 702
      removed outlier: 3.615A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.973A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA B 710 " --> pdb=" O   PRO B 706 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE B 717 " --> pdb=" O   ILE B 713 " (cutoff:3.500A)
      removed outlier: 3.731A  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 739 through 758
      removed outlier: 3.839A  pdb=" N   LEU B 743 " --> pdb=" O   GLY B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 785
    Processing helix  chain 'B' and resid 789 through 810
      removed outlier: 3.767A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE B 796 " --> pdb=" O   GLY B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 819
      removed outlier: 3.868A  pdb=" N   PHE B 814 " --> pdb=" O   GLU B 811 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 848
      removed outlier: 4.121A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA B 828 " --> pdb=" O   GLN B 824 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 839 " --> pdb=" O   PHE B 835 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LYS B 842 " --> pdb=" O   GLU B 838 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU B 843 " --> pdb=" O   THR B 839 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL B 844 " --> pdb=" O   PHE B 840 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS B 845 " --> pdb=" O   TYR B 841 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE B 846 " --> pdb=" O   LYS B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 900 through 923
      removed outlier: 3.773A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 938
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.778A  pdb=" N   ILE B 942 " --> pdb=" O   PHE B 938 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 990 through 997
      removed outlier: 3.871A  pdb=" N   MET B 994 " --> pdb=" O   PRO B 990 " (cutoff:3.500A)
      removed outlier: 3.693A  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)
    Processing helix  chain 'B' and resid 1035 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 1057 through 1067
    Processing helix  chain 'B' and resid 1090 through 1102
      removed outlier: 4.104A  pdb=" N   LEU B1094 " --> pdb=" O   ARG B1090 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1113
      removed outlier: 3.549A  pdb=" N   GLN B1112 " --> pdb=" O   LEU B1109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1114 through 1129
      removed outlier: 4.004A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY B1120 " --> pdb=" O   ALA B1116 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1133 through 1144
      removed outlier: 3.591A  pdb=" N   GLU B1137 " --> pdb=" O   ILE B1133 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU B1142 " --> pdb=" O   ARG B1138 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU B1143 " --> pdb=" O   LEU B1139 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   MET B1144 " --> pdb=" O   HIS B1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.620A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.656A  pdb=" N   LYS B1156 " --> pdb=" O   VAL B1152 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LYS B1157 " --> pdb=" O   THR B1153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1152 through 1157'
    Processing helix  chain 'B' and resid 1160 through 1183
      removed outlier: 3.610A  pdb=" N   HIS B1164 " --> pdb=" O   THR B1160 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU B1165 " --> pdb=" O   LEU B1161 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   PHE B1166 " --> pdb=" O   ARG B1162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1188 through 1195
    Processing helix  chain 'B' and resid 1195 through 1208
      removed outlier: 3.582A  pdb=" N   LEU B1199 " --> pdb=" O   LEU B1195 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU B1204 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   THR B1205 " --> pdb=" O   MET B1201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1209 through 1217
      removed outlier: 3.639A  pdb=" N   ASP B1217 " --> pdb=" O   MET B1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 690
    Processing helix  chain 'A' and resid 692 through 694
      No H-bonds generated for 'chain 'A' and resid 692 through 694'
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 3.963A  pdb=" N   ASP A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 735
      removed outlier: 3.999A  pdb=" N   ALA A 710 " --> pdb=" O   PRO A 706 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 711 " --> pdb=" O   GLN A 707 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   SER A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 3.862A  pdb=" N   GLN A 735 " --> pdb=" O   GLY A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 757
      removed outlier: 3.558A  pdb=" N   VAL A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 785
    Processing helix  chain 'A' and resid 788 through 811
      removed outlier: 3.767A  pdb=" N   TRP A 799 " --> pdb=" O   TRP A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 819
      removed outlier: 3.548A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 845
      removed outlier: 3.589A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ILE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR A 839 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS A 842 " --> pdb=" O   GLU A 838 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 850
      removed outlier: 3.916A  pdb=" N   GLU A 849 " --> pdb=" O   LYS A 845 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   HIS A 850 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 845 through 850'
    Processing helix  chain 'A' and resid 899 through 923
      removed outlier: 3.624A  pdb=" N   LEU A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER A 904 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 938
    Processing helix  chain 'A' and resid 939 through 954
      removed outlier: 3.533A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 994
    Processing helix  chain 'A' and resid 998 through 1020
    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 1058 through 1068
    Processing helix  chain 'A' and resid 1093 through 1102
      removed outlier: 3.620A  pdb=" N   LEU A1099 " --> pdb=" O   LEU A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1111
    Processing helix  chain 'A' and resid 1114 through 1129
      removed outlier: 4.358A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1142
      removed outlier: 3.677A  pdb=" N   GLU A1137 " --> pdb=" O   ILE A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1144
      No H-bonds generated for 'chain 'A' and resid 1143 through 1144'
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.693A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 3.970A  pdb=" N   LYS A1156 " --> pdb=" O   VAL A1152 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS A1157 " --> pdb=" O   THR A1153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1152 through 1157'
    Processing helix  chain 'A' and resid 1159 through 1183
      removed outlier: 3.899A  pdb=" N   CYS A1173 " --> pdb=" O   LEU A1169 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A1174 " --> pdb=" O   GLN A1170 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A1182 " --> pdb=" O   TRP A1178 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR A1183 " --> pdb=" O   ALA A1179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1208
      removed outlier: 3.795A  pdb=" N   ILE A1192 " --> pdb=" O   ALA A1188 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A1193 " --> pdb=" O   PHE A1189 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A1194 " --> pdb=" O   PRO A1190 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   VAL A1197 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      Proline residue:  A1198  - end of helix
      removed outlier: 4.322A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1211 through 1216
      removed outlier: 3.641A  pdb=" N   CYS A1215 " --> pdb=" O   ARG A1211 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 765 through 766
      removed outlier: 3.641A  pdb=" N   ALA B1055 " --> pdb=" O   GLY B 766 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 1070 through 1071
    Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 766
      removed outlier: 4.462A  pdb=" N   VAL A 764 " --> pdb=" O   ALA A1057 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA A1055 " --> pdb=" O   GLY A 766 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1281 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: 2.15

  Time building geometry restraints manager: 3.28 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: 2460
        1.34 -     1.46: 1796
        1.46 -     1.58: 3920
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8254
  Sorted by residual:
  bond pdb=" C   LYS B 893 "
       pdb=" N   PRO B 894 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.34e-02 5.57e+03 3.06e+00
  bond pdb=" CB  MET A1042 "
       pdb=" CG  MET A1042 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.28e-01
  bond pdb=" CB  PHE A1122 "
       pdb=" CG  PHE A1122 "
    ideal  model  delta    sigma   weight residual
    1.502  1.482  0.020 2.30e-02 1.89e+03 7.87e-01
  bond pdb=" N   PHE B 916 "
       pdb=" CA  PHE B 916 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.010 1.21e-02 6.83e+03 7.41e-01
  bond pdb=" C   SER A 721 "
       pdb=" N   PRO A 722 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.36e-02 5.41e+03 7.22e-01
  ... (remaining 8249 not shown)

  Histogram of bond angle deviations from ideal:
       99.47 -   106.39: 263
      106.39 -   113.31: 4544
      113.31 -   120.24: 3105
      120.24 -   127.16: 3198
      127.16 -   134.09: 92
  Bond angle restraints: 11202
  Sorted by residual:
  angle pdb=" CB  MET B1213 "
        pdb=" CG  MET B1213 "
        pdb=" SD  MET B1213 "
      ideal   model   delta    sigma   weight residual
     112.70  121.03   -8.33 3.00e+00 1.11e-01 7.71e+00
  angle pdb=" N   PHE B 916 "
        pdb=" CA  PHE B 916 "
        pdb=" CB  PHE B 916 "
      ideal   model   delta    sigma   weight residual
     110.12  114.17   -4.05 1.47e+00 4.63e-01 7.58e+00
  angle pdb=" C   ARG A 692 "
        pdb=" N   TYR A 693 "
        pdb=" CA  TYR A 693 "
      ideal   model   delta    sigma   weight residual
     120.09  123.20   -3.11 1.25e+00 6.40e-01 6.20e+00
  angle pdb=" N   TYR A 789 "
        pdb=" CA  TYR A 789 "
        pdb=" C   TYR A 789 "
      ideal   model   delta    sigma   weight residual
     110.80  115.81   -5.01 2.13e+00 2.20e-01 5.53e+00
  angle pdb=" N   TYR B 693 "
        pdb=" CA  TYR B 693 "
        pdb=" C   TYR B 693 "
      ideal   model   delta    sigma   weight residual
     109.81  114.94   -5.13 2.21e+00 2.05e-01 5.39e+00
  ... (remaining 11197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4389
       17.90 -    35.79: 413
       35.79 -    53.69: 58
       53.69 -    71.58: 10
       71.58 -    89.48: 11
  Dihedral angle restraints: 4881
    sinusoidal: 1943
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CA  SER A1182 "
           pdb=" C   SER A1182 "
           pdb=" N   THR A1183 "
           pdb=" CA  THR A1183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.52  -17.48     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  GLY B1107 "
           pdb=" C   GLY B1107 "
           pdb=" N   ASP B1108 "
           pdb=" CA  ASP B1108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.54   17.46     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  MET A1213 "
           pdb=" C   MET A1213 "
           pdb=" N   LYS A1214 "
           pdb=" CA  LYS A1214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.04   16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 4878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 883
       0.038 -    0.077: 347
       0.077 -    0.115: 87
       0.115 -    0.154: 8
       0.154 -    0.192: 3
  Chirality restraints: 1328
  Sorted by residual:
  chirality pdb=" CA  PHE B 916 "
            pdb=" N   PHE B 916 "
            pdb=" C   PHE B 916 "
            pdb=" CB  PHE B 916 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.24e-01
  chirality pdb=" CA  ILE A 738 "
            pdb=" N   ILE A 738 "
            pdb=" C   ILE A 738 "
            pdb=" CB  ILE A 738 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.20e-01
  chirality pdb=" CB  THR A1183 "
            pdb=" CA  THR A1183 "
            pdb=" OG1 THR A1183 "
            pdb=" CG2 THR A1183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 1325 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 916 "   -0.031 2.00e-02 2.50e+03   2.53e-02 1.12e+01
        pdb=" CG  PHE B 916 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 916 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 916 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 916 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 916 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 916 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 693 "    0.039 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO B 694 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 694 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 694 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 893 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO B 894 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 894 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 894 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 45
        2.67 -     3.23: 7622
        3.23 -     3.79: 11657
        3.79 -     4.34: 15078
        4.34 -     4.90: 26275
  Nonbonded interactions: 60677
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 820 "
            pdb=" NH1 ARG A1200 "
     model   vdw
     2.113 2.520
  nonbonded pdb=" O   LYS B 922 "
            pdb=" NH1 ARG B 933 "
     model   vdw
     2.327 2.520
  nonbonded pdb=" NE2 GLN B1089 "
            pdb=" OG1 THR B1092 "
     model   vdw
     2.342 2.520
  nonbonded pdb=" OE1 GLU B 775 "
            pdb=" OH  TYR B 789 "
     model   vdw
     2.350 2.440
  nonbonded pdb=" OD1 ASP A 699 "
            pdb=" NZ  LYS A1028 "
     model   vdw
     2.358 2.520
  ... (remaining 60672 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' and (resid 673 through 855 or resid 894 through 1219))
}

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:             0.700
  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:          3.900
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.390
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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      :  0.003   0.029   8254  Z= 0.224
  Angle     :  0.623   8.330  11202  Z= 0.316
  Chirality :  0.042   0.192   1328
  Planarity :  0.005   0.060   1374
  Dihedral  : 14.331  89.477   2981
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    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:  0.31 (0.28), residues: 1012
  helix:  1.03 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.27 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 992 
 HIS   0.007   0.001   HIS A1064 
 PHE   0.058   0.002   PHE B 916 
 TYR   0.008   0.001   TYR B1154 
 ARG   0.008   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.865 
Fit side-chains
REVERT: B 1157 LYS cc_start: 0.8708 (mppt) cc_final: 0.8354 (mptt)
REVERT: A 1157 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8318 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1934
  time to fit residues: 37.0205
Evaluate side-chains
  121 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 735 GLN
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.0665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8254  Z= 0.216
  Angle     :  0.572   7.079  11202  Z= 0.285
  Chirality :  0.041   0.151   1328
  Planarity :  0.005   0.060   1374
  Dihedral  :  4.093  18.665   1094
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  7.08 %
    Favored  : 91.44 %
  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:  0.48 (0.28), residues: 1012
  helix:  1.21 (0.22), residues: 649
  sheet:  None (None), residues: 0
  loop : -1.31 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 992 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.016   0.001   PHE A1122 
 TYR   0.009   0.001   TYR B1124 
 ARG   0.003   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B 1071 MET cc_start: 0.7900 (mmm) cc_final: 0.7557 (mtt)
REVERT: B 1157 LYS cc_start: 0.8682 (mppt) cc_final: 0.8365 (mptt)
REVERT: A 1157 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8337 (mmmt)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.2112
  time to fit residues: 36.2677
Evaluate side-chains
  127 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  686 ILE
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1176 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0070
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
B 735 GLN
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.0849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8254  Z= 0.174
  Angle     :  0.526   7.105  11202  Z= 0.263
  Chirality :  0.039   0.154   1328
  Planarity :  0.005   0.059   1374
  Dihedral  :  3.970  18.329   1094
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  9.13 %
    Favored  : 88.93 %
  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:  0.65 (0.28), residues: 1012
  helix:  1.42 (0.22), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.39 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 992 
 HIS   0.004   0.001   HIS A1064 
 PHE   0.014   0.001   PHE A1189 
 TYR   0.009   0.001   TYR B1124 
 ARG   0.006   0.000   ARG A 821 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B  916 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7521 (t80)
REVERT: B 1157 LYS cc_start: 0.8707 (mppt) cc_final: 0.8383 (mptt)
REVERT: A 1157 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8349 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 132
  average time/residue: 0.2038
  time to fit residues: 36.9640
Evaluate side-chains
  131 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1199 LEU
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  979 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 87 optimal weight:    0.3980
   chunk 26 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 735 GLN
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8254  Z= 0.195
  Angle     :  0.532   6.985  11202  Z= 0.265
  Chirality :  0.040   0.151   1328
  Planarity :  0.005   0.058   1374
  Dihedral  :  3.954  18.200   1094
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.73 %
    Favored  : 87.33 %
  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:  0.72 (0.28), residues: 1012
  helix:  1.50 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.41 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 992 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.005   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.903 
Fit side-chains
REVERT: B  916 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7568 (t80)
REVERT: B 1157 LYS cc_start: 0.8729 (mppt) cc_final: 0.8386 (mptt)
  outliers start: 17
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2034
  time to fit residues: 36.0022
Evaluate side-chains
  132 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain B residue 1180 VAL
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1199 LEU
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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: 0.7728
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8254  Z= 0.349
  Angle     :  0.626   7.333  11202  Z= 0.314
  Chirality :  0.043   0.159   1328
  Planarity :  0.005   0.058   1374
  Dihedral  :  4.262  19.934   1094
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.36 %
    Favored  : 84.47 %
  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:  0.38 (0.27), residues: 1012
  helix:  1.19 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.48 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 992 
 HIS   0.010   0.001   HIS A1064 
 PHE   0.018   0.002   PHE A 835 
 TYR   0.015   0.002   TYR B1124 
 ARG   0.007   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.111 
Fit side-chains
REVERT: B  916 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7618 (t80)
REVERT: B 1157 LYS cc_start: 0.8718 (mppt) cc_final: 0.8329 (mptt)
REVERT: A  733 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6744 (tptm)
REVERT: A 1195 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7825 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1959
  time to fit residues: 33.6695
Evaluate side-chains
  128 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain B residue 1180 VAL
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1201 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain A residue  918 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.0170
   chunk 19 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 94 optimal weight:    0.0020
   overall best weight:    0.4426

-------------------------------------------------------------------------------
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**
A 750 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8254  Z= 0.154
  Angle     :  0.516   7.287  11202  Z= 0.257
  Chirality :  0.039   0.149   1328
  Planarity :  0.004   0.057   1374
  Dihedral  :  3.991  18.875   1094
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.95 %
    Favored  : 83.45 %
  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:  0.76 (0.28), residues: 1012
  helix:  1.51 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 992 
 HIS   0.002   0.000   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.007   0.001   TYR B1124 
 ARG   0.005   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: B  916 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7574 (t80)
REVERT: B  952 TYR cc_start: 0.8107 (t80) cc_final: 0.7836 (t80)
REVERT: A 1195 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7665 (mp)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1812
  time to fit residues: 32.7446
Evaluate side-chains
  127 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0970
   chunk 82 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7618

-------------------------------------------------------------------------------
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: 0.7657
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8254  Z= 0.189
  Angle     :  0.537   7.308  11202  Z= 0.266
  Chirality :  0.040   0.151   1328
  Planarity :  0.005   0.058   1374
  Dihedral  :  3.960  18.660   1094
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.75 %
    Favored  : 82.53 %
  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:  0.77 (0.28), residues: 1012
  helix:  1.52 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -1.36 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 992 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.010   0.001   TYR B1124 
 ARG   0.007   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: B  916 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7582 (t80)
REVERT: B  952 TYR cc_start: 0.8113 (t80) cc_final: 0.7850 (t80)
REVERT: A  993 MET cc_start: 0.5952 (mmp) cc_final: 0.5620 (mpp)
REVERT: A 1195 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7724 (mp)
  outliers start: 15
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1934
  time to fit residues: 32.8693
Evaluate side-chains
  129 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1201 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0010
   chunk 88 optimal weight:    0.0970
   chunk 93 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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: 0.7620
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8254  Z= 0.153
  Angle     :  0.518   7.514  11202  Z= 0.255
  Chirality :  0.039   0.154   1328
  Planarity :  0.004   0.058   1374
  Dihedral  :  3.838  18.786   1094
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.87 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.28), residues: 1012
  helix:  1.65 (0.21), residues: 645
  sheet:  None (None), residues: 0
  loop : -1.30 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 992 
 HIS   0.003   0.001   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.007   0.001   TYR B1124 
 ARG   0.008   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
REVERT: B  916 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7573 (t80)
REVERT: B  952 TYR cc_start: 0.8098 (t80) cc_final: 0.7848 (t80)
REVERT: A  817 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7311 (ttm110)
REVERT: A  993 MET cc_start: 0.5694 (mmp) cc_final: 0.5453 (mpp)
REVERT: A 1195 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7664 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 127
  average time/residue: 0.2122
  time to fit residues: 37.5394
Evaluate side-chains
  132 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue  974 GLU
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1201 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0770
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.0540

-------------------------------------------------------------------------------
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: 0.7678
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8254  Z= 0.235
  Angle     :  0.562   7.701  11202  Z= 0.279
  Chirality :  0.041   0.154   1328
  Planarity :  0.005   0.058   1374
  Dihedral  :  3.960  18.381   1094
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.32 %
    Favored  : 82.08 %
  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:  0.80 (0.28), residues: 1012
  helix:  1.55 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -1.36 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 992 
 HIS   0.007   0.001   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.013   0.001   TYR B1124 
 ARG   0.008   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: B  916 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7599 (t80)
REVERT: B  952 TYR cc_start: 0.8124 (t80) cc_final: 0.7872 (t80)
REVERT: A  817 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7380 (ttp80)
REVERT: A 1195 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7654 (mp)
  outliers start: 14
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1976
  time to fit residues: 34.2253
Evaluate side-chains
  131 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1151 ASP
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1201 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0570
   chunk 24 optimal weight:    0.0370
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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: 0.7623
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8254  Z= 0.153
  Angle     :  0.526   8.064  11202  Z= 0.258
  Chirality :  0.039   0.161   1328
  Planarity :  0.004   0.058   1374
  Dihedral  :  3.842  18.529   1094
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.44 %
    Favored  : 81.96 %
  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:  0.97 (0.28), residues: 1012
  helix:  1.68 (0.21), residues: 645
  sheet:  None (None), residues: 0
  loop : -1.28 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 992 
 HIS   0.002   0.001   HIS A1064 
 PHE   0.014   0.001   PHE A1189 
 TYR   0.008   0.001   TYR B1124 
 ARG   0.008   0.000   ARG B 701 

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: B  916 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7593 (t80)
REVERT: B  952 TYR cc_start: 0.8103 (t80) cc_final: 0.7859 (t80)
REVERT: A  817 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7386 (ttp80)
REVERT: A 1195 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7667 (mp)
  outliers start: 14
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1879
  time to fit residues: 32.1970
Evaluate side-chains
  130 residues out of total 876 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue 1022 LYS
Chi-restraints excluded: chain B residue 1183 THR
Chi-restraints excluded: chain B residue 1201 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1108 ASP
Chi-restraints excluded: chain A residue 1122 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 70 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.183068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139019 restraints weight = 8196.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.31
r_work: 0.3331 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8254  Z= 0.192
  Angle     :  0.543   8.187  11202  Z= 0.268
  Chirality :  0.040   0.158   1328
  Planarity :  0.004   0.058   1374
  Dihedral  :  3.872  18.219   1094
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.44 %
    Favored  : 81.96 %
  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:  0.93 (0.28), residues: 1012
  helix:  1.66 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.32 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 992 
 HIS   0.005   0.001   HIS A1064 
 PHE   0.015   0.001   PHE A1189 
 TYR   0.011   0.001   TYR B1124 
 ARG   0.008   0.000   ARG B 701 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1927.84 seconds
wall clock time: 35 minutes 29.12 seconds (2129.12 seconds total)