Starting phenix.real_space_refine
on Wed Sep 17 07:25:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u3r_63825/09_2025/9u3r_63825.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.028
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      49      5.16       5
     C    4339      2.51       5
     N    1100      2.21       5
     O    1202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6690
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 847, 6690
          Classifications: {'peptide': 847}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 824}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 1.88, per 1000 atoms: 0.28
  Number of scatterers: 6690
  At special positions: 0
  Unit cell: (63.63, 89.89, 148.47, 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      49     16.00
     O    1202      8.00
     N    1100      7.00
     C    4339      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 268 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 425.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      68.6% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 138
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 145 through 165
      removed outlier: 4.036A  pdb=" N   ALA A 149 " --> pdb=" O   MET A 145 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 171
      removed outlier: 3.787A  pdb=" N   ALA A 169 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG A 170 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 194
      removed outlier: 3.668A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   VAL A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 3.964A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 263
    Processing helix  chain 'A' and resid 279 through 336
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 411 through 434
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.519A  pdb=" N   LYS A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 523
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.933A  pdb=" N   TYR A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 555
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.753A  pdb=" N   LEU A 563 " --> pdb=" O   ALA A 560 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS A 564 " --> pdb=" O   ASP A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 564'
    Processing helix  chain 'A' and resid 756 through 765
    Processing helix  chain 'A' and resid 765 through 774
    Processing helix  chain 'A' and resid 782 through 810
      removed outlier: 3.533A  pdb=" N   TYR A 809 " --> pdb=" O   CYS A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 843
    Processing helix  chain 'A' and resid 849 through 860
      removed outlier: 3.629A  pdb=" N   LEU A 855 " --> pdb=" O   CYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 882
      removed outlier: 3.867A  pdb=" N   ILE A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      Proline residue:  A 876  - end of helix
    Processing helix  chain 'A' and resid 883 through 884
      No H-bonds generated for 'chain 'A' and resid 883 through 884'
    Processing helix  chain 'A' and resid 885 through 889
      removed outlier: 4.384A  pdb=" N   GLU A 889 " --> pdb=" O   SER A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 909
      removed outlier: 3.791A  pdb=" N   ILE A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 929 through 937
      removed outlier: 3.683A  pdb=" N   VAL A 937 " --> pdb=" O   LEU A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 1034
    Processing helix  chain 'A' and resid 1037 through 1045
      removed outlier: 3.576A  pdb=" N   ALA A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLU A1042 " --> pdb=" O   TYR A1038 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   GLN A1043 " --> pdb=" O   HIS A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1071
    Processing helix  chain 'A' and resid 1081 through 1097
      removed outlier: 3.547A  pdb=" N   LEU A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1102
      removed outlier: 3.804A  pdb=" N   SER A1102 " --> pdb=" O   PRO A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1132 through 1154
      removed outlier: 3.573A  pdb=" N   ASN A1154 " --> pdb=" O   ASP A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1200
      removed outlier: 3.538A  pdb=" N   ASP A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1220
      removed outlier: 3.976A  pdb=" N   VAL A1215 " --> pdb=" O   GLU A1211 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LYS A1218 " --> pdb=" O   ARG A1214 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   MET A1219 " --> pdb=" O   VAL A1215 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.607A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.607A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS A 528 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A 492 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498
      removed outlier: 3.849A  pdb=" N   GLY A 498 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP A 508 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 4.826A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A1175 " --> pdb=" O   ASP A1185 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A1185 " --> pdb=" O   GLY A1175 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 4.826A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL A1165 " --> pdb=" O   GLN A1207 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   GLY A1235 " --> pdb=" O   ASN A1230 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   ASN A1230 " --> pdb=" O   GLY A1235 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   MET A1237 " --> pdb=" O   THR A1228 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   THR A1228 " --> pdb=" O   MET A1237 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   THR A1239 " --> pdb=" O   ARG A1226 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A1226 " --> pdb=" O   THR A1239 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1389 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: 1.18

  Time building geometry restraints manager: 0.75 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: 2116
        1.34 -     1.46: 1304
        1.46 -     1.58: 3348
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 6840
  Sorted by residual:
  bond pdb=" CB  GLN A 220 "
       pdb=" CG  GLN A 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.50e+00
  bond pdb=" CB  GLN A 303 "
       pdb=" CG  GLN A 303 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.77e-01
  bond pdb=" CG  ARG A 340 "
       pdb=" CD  ARG A 340 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.53e-01
  bond pdb=" CG  GLN A 303 "
       pdb=" CD  GLN A 303 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.19e-01
  bond pdb=" CA  ASN A1053 "
       pdb=" CB  ASN A1053 "
    ideal  model  delta    sigma   weight residual
    1.531  1.546 -0.015 1.58e-02 4.01e+03 8.97e-01
  ... (remaining 6835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 9113
        1.76 -     3.53: 110
        3.53 -     5.29: 32
        5.29 -     7.06: 10
        7.06 -     8.82: 2
  Bond angle restraints: 9267
  Sorted by residual:
  angle pdb=" CA  LYS A 773 "
        pdb=" CB  LYS A 773 "
        pdb=" CG  LYS A 773 "
      ideal   model   delta    sigma   weight residual
     114.10  121.08   -6.98 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" N   VAL A 337 "
        pdb=" CA  VAL A 337 "
        pdb=" C   VAL A 337 "
      ideal   model   delta    sigma   weight residual
     113.53  110.15    3.38 9.80e-01 1.04e+00 1.19e+01
  angle pdb=" CA  LYS A 808 "
        pdb=" CB  LYS A 808 "
        pdb=" CG  LYS A 808 "
      ideal   model   delta    sigma   weight residual
     114.10  120.22   -6.12 2.00e+00 2.50e-01 9.37e+00
  angle pdb=" N   GLU A1203 "
        pdb=" CA  GLU A1203 "
        pdb=" C   GLU A1203 "
      ideal   model   delta    sigma   weight residual
     109.15  113.31   -4.16 1.44e+00 4.82e-01 8.34e+00
  angle pdb=" CB  GLN A 303 "
        pdb=" CG  GLN A 303 "
        pdb=" CD  GLN A 303 "
      ideal   model   delta    sigma   weight residual
     112.60  117.28   -4.68 1.70e+00 3.46e-01 7.58e+00
  ... (remaining 9262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 3332
       16.78 -    33.55: 494
       33.55 -    50.33: 147
       50.33 -    67.10: 27
       67.10 -    83.88: 9
  Dihedral angle restraints: 4009
    sinusoidal: 1540
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" CG  ARG A 487 "
           pdb=" CD  ARG A 487 "
           pdb=" NE  ARG A 487 "
           pdb=" CZ  ARG A 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.93  -44.93     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.83  -16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CB  GLU A1203 "
           pdb=" CG  GLU A1203 "
           pdb=" CD  GLU A1203 "
           pdb=" OE1 GLU A1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.88   83.88     1      3.00e+01 1.11e-03 9.53e+00
  ... (remaining 4006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 739
       0.031 -    0.061: 233
       0.061 -    0.092: 64
       0.092 -    0.122: 23
       0.122 -    0.153: 3
  Chirality restraints: 1062
  Sorted by residual:
  chirality pdb=" CA  ARG A1205 "
            pdb=" N   ARG A1205 "
            pdb=" C   ARG A1205 "
            pdb=" CB  ARG A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  ILE A 499 "
            pdb=" N   ILE A 499 "
            pdb=" C   ILE A 499 "
            pdb=" CB  ILE A 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ILE A 747 "
            pdb=" N   ILE A 747 "
            pdb=" C   ILE A 747 "
            pdb=" CB  ILE A 747 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 510 "   -0.022 2.00e-02 2.50e+03   1.64e-02 6.74e+00
        pdb=" CG  TRP A 510 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 510 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 510 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 510 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 510 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 510 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 510 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 510 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 510 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 240 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 241 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 930 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 931 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 931 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 931 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 197
        2.72 -     3.26: 7045
        3.26 -     3.81: 11260
        3.81 -     4.35: 13786
        4.35 -     4.90: 22710
  Nonbonded interactions: 54998
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A1205 "
            pdb=" O   TYR A1242 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR A 809 "
            pdb=" O   HIS A 883 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" ND2 ASN A1066 "
            pdb=" O   ASN A1160 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   LEU A 799 "
            pdb=" OG1 THR A 803 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE1 GLU A 770 "
            pdb=" OG1 THR A 784 "
     model   vdw
     2.251 3.040
  ... (remaining 54993 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.640
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6293
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   0.037   6841  Z= 0.111
  Angle     :  0.575   8.820   9269  Z= 0.304
  Chirality :  0.035   0.153   1062
  Planarity :  0.004   0.045   1157
  Dihedral  : 17.683  83.880   2410
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 30.65 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.29), residues: 827
  helix:  1.28 (0.22), residues: 511
  sheet: -0.75 (0.69), residues: 58
  loop : -0.23 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 340 
 TYR   0.021   0.001   TYR A 261 
 PHE   0.013   0.001   PHE A 507 
 TRP   0.044   0.002   TRP A 510 
 HIS   0.005   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6840)
  covalent geometry    : angle       0.57486 ( 9267)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.21053 (    2)
  hydrogen bonds       : bond        0.23294 (  458)
  hydrogen bonds       : angle       7.92892 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 PHE cc_start: 0.8050 (t80) cc_final: 0.7806 (t80)
REVERT: A  302 SER cc_start: 0.7646 (t) cc_final: 0.7212 (p)
REVERT: A 1002 VAL cc_start: 0.8448 (m) cc_final: 0.8180 (p)
REVERT: A 1004 TYR cc_start: 0.8219 (t80) cc_final: 0.7845 (t80)
REVERT: A 1029 ASP cc_start: 0.7313 (m-30) cc_final: 0.6992 (m-30)
REVERT: A 1033 ARG cc_start: 0.6752 (tpp80) cc_final: 0.6539 (mpp80)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1187
  time to fit residues: 21.3330
Evaluate side-chains
  131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
A 475 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS
A1017 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.186126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.164011 restraints weight = 10320.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 2.22
r_work: 0.3975 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6841  Z= 0.159
  Angle     :  0.577   7.683   9269  Z= 0.303
  Chirality :  0.040   0.158   1062
  Planarity :  0.004   0.042   1157
  Dihedral  :  3.962  17.837    910
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 27.18 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.29), residues: 827
  helix:  1.66 (0.22), residues: 540
  sheet: -0.63 (0.63), residues: 66
  loop : -0.85 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 840 
 TYR   0.021   0.002   TYR A1050 
 PHE   0.019   0.002   PHE A 897 
 TRP   0.013   0.001   TRP A 510 
 HIS   0.005   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6840)
  covalent geometry    : angle       0.57689 ( 9267)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.30726 (    2)
  hydrogen bonds       : bond        0.04635 (  458)
  hydrogen bonds       : angle       5.09965 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  146 VAL cc_start: 0.7645 (p) cc_final: 0.7320 (m)
REVERT: A  193 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6326 (mp10)
REVERT: A  223 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7749 (p)
REVERT: A  224 PHE cc_start: 0.8124 (t80) cc_final: 0.7886 (t80)
REVERT: A  229 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: A  395 ILE cc_start: 0.7045 (mt) cc_final: 0.6788 (mp)
REVERT: A  410 LYS cc_start: 0.3280 (mttm) cc_final: 0.2442 (mttm)
REVERT: A 1002 VAL cc_start: 0.8765 (m) cc_final: 0.8463 (p)
REVERT: A 1145 MET cc_start: 0.5325 (tpp) cc_final: 0.5051 (mtp)
  outliers start: 24
  outliers final: 6
  residues processed: 166
  average time/residue: 0.0991
  time to fit residues: 21.1247
Evaluate side-chains
  142 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1167 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.0270
   chunk 48 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0570
   chunk 64 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0070
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 ASN
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.188723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.166519 restraints weight = 10263.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 2.22
r_work: 0.4023 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6841  Z= 0.119
  Angle     :  0.534  11.037   9269  Z= 0.274
  Chirality :  0.038   0.147   1062
  Planarity :  0.004   0.041   1157
  Dihedral  :  3.884  16.217    910
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.35 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.29), residues: 827
  helix:  1.88 (0.22), residues: 539
  sheet: -0.37 (0.65), residues: 66
  loop : -0.88 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 340 
 TYR   0.018   0.001   TYR A1050 
 PHE   0.011   0.001   PHE A 403 
 TRP   0.014   0.001   TRP A 510 
 HIS   0.004   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6840)
  covalent geometry    : angle       0.53406 ( 9267)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.19554 (    2)
  hydrogen bonds       : bond        0.04018 (  458)
  hydrogen bonds       : angle       4.70418 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  146 VAL cc_start: 0.7585 (p) cc_final: 0.7249 (m)
REVERT: A  220 GLN cc_start: 0.6665 (tm-30) cc_final: 0.6425 (tm-30)
REVERT: A  223 SER cc_start: 0.8134 (m) cc_final: 0.7718 (p)
REVERT: A  229 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7244 (mt-10)
REVERT: A  395 ILE cc_start: 0.7064 (mt) cc_final: 0.6810 (mp)
REVERT: A  396 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6253 (mt)
REVERT: A  410 LYS cc_start: 0.2808 (mttm) cc_final: 0.1835 (mtpp)
REVERT: A 1002 VAL cc_start: 0.8687 (m) cc_final: 0.8392 (p)
REVERT: A 1145 MET cc_start: 0.5340 (tpp) cc_final: 0.5095 (mtp)
  outliers start: 23
  outliers final: 10
  residues processed: 156
  average time/residue: 0.1033
  time to fit residues: 20.6731
Evaluate side-chains
  145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 61 optimal weight:    0.4980
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 ASN
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
A 997 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.185378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.163223 restraints weight = 10296.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 2.25
r_work: 0.3964 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6841  Z= 0.159
  Angle     :  0.554   7.945   9269  Z= 0.286
  Chirality :  0.040   0.169   1062
  Planarity :  0.004   0.039   1157
  Dihedral  :  3.992  15.826    910
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 26.07 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.29), residues: 827
  helix:  1.81 (0.22), residues: 545
  sheet: -0.17 (0.66), residues: 66
  loop : -1.03 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 340 
 TYR   0.011   0.001   TYR A1114 
 PHE   0.012   0.002   PHE A 224 
 TRP   0.021   0.002   TRP A 510 
 HIS   0.004   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6840)
  covalent geometry    : angle       0.55392 ( 9267)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.31235 (    2)
  hydrogen bonds       : bond        0.03902 (  458)
  hydrogen bonds       : angle       4.65710 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  146 VAL cc_start: 0.7578 (p) cc_final: 0.7270 (m)
REVERT: A  193 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.5948 (mp10)
REVERT: A  223 SER cc_start: 0.8311 (m) cc_final: 0.7903 (p)
REVERT: A  229 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: A  326 GLU cc_start: 0.7005 (tt0) cc_final: 0.6466 (tt0)
REVERT: A  532 SER cc_start: 0.7151 (t) cc_final: 0.6520 (m)
REVERT: A  833 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7579 (mm)
REVERT: A 1002 VAL cc_start: 0.8695 (m) cc_final: 0.8399 (p)
REVERT: A 1025 ARG cc_start: 0.6990 (tpp80) cc_final: 0.6641 (tpp80)
REVERT: A 1145 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.4852 (ttp)
  outliers start: 30
  outliers final: 15
  residues processed: 166
  average time/residue: 0.0971
  time to fit residues: 20.9119
Evaluate side-chains
  160 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.0270
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0970
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5636

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.180260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.157629 restraints weight = 10265.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 2.30
r_work: 0.3969 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6841  Z= 0.138
  Angle     :  0.540   8.004   9269  Z= 0.277
  Chirality :  0.040   0.202   1062
  Planarity :  0.004   0.044   1157
  Dihedral  :  3.955  16.585    910
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 27.05 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.29), residues: 827
  helix:  1.91 (0.22), residues: 543
  sheet: -0.15 (0.68), residues: 66
  loop : -1.11 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.010   0.001   TYR A1114 
 PHE   0.016   0.001   PHE A 780 
 TRP   0.016   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6840)
  covalent geometry    : angle       0.53983 ( 9267)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.21547 (    2)
  hydrogen bonds       : bond        0.03731 (  458)
  hydrogen bonds       : angle       4.59304 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.3116 (OUTLIER) cc_final: 0.2382 (mm-30)
REVERT: A  146 VAL cc_start: 0.7570 (p) cc_final: 0.7277 (m)
REVERT: A  193 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.5907 (mp10)
REVERT: A  223 SER cc_start: 0.8211 (m) cc_final: 0.7871 (p)
REVERT: A  234 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8156 (tp)
REVERT: A  246 LEU cc_start: 0.8181 (tp) cc_final: 0.7963 (tt)
REVERT: A  305 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7965 (ttm110)
REVERT: A  326 GLU cc_start: 0.6963 (tt0) cc_final: 0.6441 (tt0)
REVERT: A  532 SER cc_start: 0.7161 (t) cc_final: 0.6550 (m)
REVERT: A  833 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7544 (mm)
REVERT: A  840 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.7151 (tpt-90)
REVERT: A 1002 VAL cc_start: 0.8673 (m) cc_final: 0.8361 (p)
REVERT: A 1025 ARG cc_start: 0.7001 (tpp80) cc_final: 0.6769 (tpp80)
REVERT: A 1145 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.4908 (ttp)
  outliers start: 30
  outliers final: 21
  residues processed: 170
  average time/residue: 0.0982
  time to fit residues: 21.2376
Evaluate side-chains
  169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0970
   chunk 31 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN
A1009 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.179788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.157143 restraints weight = 10199.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.29
r_work: 0.3954 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6841  Z= 0.144
  Angle     :  0.570   8.604   9269  Z= 0.287
  Chirality :  0.040   0.189   1062
  Planarity :  0.004   0.043   1157
  Dihedral  :  3.977  16.448    910
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.07 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.29), residues: 827
  helix:  1.89 (0.22), residues: 541
  sheet: -0.15 (0.67), residues: 66
  loop : -1.10 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1205 
 TYR   0.010   0.001   TYR A1114 
 PHE   0.013   0.001   PHE A 780 
 TRP   0.015   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6840)
  covalent geometry    : angle       0.56996 ( 9267)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.21742 (    2)
  hydrogen bonds       : bond        0.03717 (  458)
  hydrogen bonds       : angle       4.53396 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 147
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.2956 (OUTLIER) cc_final: 0.2252 (mm-30)
REVERT: A  146 VAL cc_start: 0.7540 (p) cc_final: 0.7247 (m)
REVERT: A  193 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.5883 (mp10)
REVERT: A  220 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6250 (tm-30)
REVERT: A  223 SER cc_start: 0.8251 (m) cc_final: 0.7928 (p)
REVERT: A  234 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8134 (tp)
REVERT: A  246 LEU cc_start: 0.8229 (tp) cc_final: 0.8014 (tt)
REVERT: A  254 VAL cc_start: 0.8237 (p) cc_final: 0.8024 (p)
REVERT: A  487 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7558 (mtp-110)
REVERT: A  532 SER cc_start: 0.7093 (t) cc_final: 0.6467 (m)
REVERT: A  760 GLU cc_start: 0.7367 (tp30) cc_final: 0.7002 (tm-30)
REVERT: A  840 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7201 (mmm160)
REVERT: A 1002 VAL cc_start: 0.8676 (m) cc_final: 0.8371 (p)
REVERT: A 1145 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4957 (ttp)
  outliers start: 43
  outliers final: 25
  residues processed: 175
  average time/residue: 0.0922
  time to fit residues: 20.9698
Evaluate side-chains
  170 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN
A1009 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.179388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.156416 restraints weight = 10140.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.27
r_work: 0.3953 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6841  Z= 0.168
  Angle     :  0.602  11.215   9269  Z= 0.303
  Chirality :  0.041   0.182   1062
  Planarity :  0.004   0.043   1157
  Dihedral  :  4.050  16.195    910
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 27.60 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.29), residues: 827
  helix:  1.84 (0.22), residues: 544
  sheet: -0.17 (0.71), residues: 59
  loop : -1.31 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 332 
 TYR   0.011   0.001   TYR A1114 
 PHE   0.013   0.001   PHE A 403 
 TRP   0.015   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6840)
  covalent geometry    : angle       0.60170 ( 9267)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.27682 (    2)
  hydrogen bonds       : bond        0.03823 (  458)
  hydrogen bonds       : angle       4.59330 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 150
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3036 (OUTLIER) cc_final: 0.2270 (mm-30)
REVERT: A  146 VAL cc_start: 0.7588 (p) cc_final: 0.7299 (m)
REVERT: A  164 PHE cc_start: 0.7605 (m-80) cc_final: 0.7326 (m-80)
REVERT: A  193 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5862 (mp10)
REVERT: A  223 SER cc_start: 0.8217 (m) cc_final: 0.7956 (p)
REVERT: A  234 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8104 (tp)
REVERT: A  246 LEU cc_start: 0.8197 (tp) cc_final: 0.7990 (tt)
REVERT: A  387 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6100 (mtm)
REVERT: A  487 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7518 (mtp-110)
REVERT: A  532 SER cc_start: 0.7101 (t) cc_final: 0.6504 (m)
REVERT: A  760 GLU cc_start: 0.7344 (tp30) cc_final: 0.6828 (tp30)
REVERT: A  773 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8293 (mmtm)
REVERT: A  840 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7247 (mmm-85)
REVERT: A  849 MET cc_start: 0.7647 (pmm) cc_final: 0.7318 (pmm)
REVERT: A 1002 VAL cc_start: 0.8698 (m) cc_final: 0.8392 (p)
REVERT: A 1025 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6768 (tpp80)
REVERT: A 1145 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.4669 (ttp)
REVERT: A 1205 ARG cc_start: 0.5399 (mmm160) cc_final: 0.4870 (mmm160)
  outliers start: 37
  outliers final: 24
  residues processed: 173
  average time/residue: 0.0999
  time to fit residues: 22.1467
Evaluate side-chains
  179 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 32 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.180217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.157180 restraints weight = 10174.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 2.30
r_work: 0.3963 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6841  Z= 0.139
  Angle     :  0.597   9.874   9269  Z= 0.297
  Chirality :  0.041   0.378   1062
  Planarity :  0.004   0.040   1157
  Dihedral  :  3.963  15.993    910
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 28.02 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.30), residues: 827
  helix:  1.90 (0.22), residues: 544
  sheet: -0.22 (0.71), residues: 59
  loop : -1.34 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 764 
 TYR   0.018   0.001   TYR A 118 
 PHE   0.019   0.001   PHE A 224 
 TRP   0.015   0.001   TRP A 510 
 HIS   0.011   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6840)
  covalent geometry    : angle       0.59673 ( 9267)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       0.34491 (    2)
  hydrogen bonds       : bond        0.03696 (  458)
  hydrogen bonds       : angle       4.52569 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.3002 (OUTLIER) cc_final: 0.2246 (mm-30)
REVERT: A  146 VAL cc_start: 0.7553 (p) cc_final: 0.7272 (m)
REVERT: A  164 PHE cc_start: 0.7649 (m-80) cc_final: 0.7352 (m-80)
REVERT: A  193 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.5784 (mp10)
REVERT: A  223 SER cc_start: 0.8209 (m) cc_final: 0.7898 (p)
REVERT: A  234 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8077 (tp)
REVERT: A  246 LEU cc_start: 0.8177 (tp) cc_final: 0.7971 (tt)
REVERT: A  387 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.5984 (mtm)
REVERT: A  487 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7498 (mtp-110)
REVERT: A  532 SER cc_start: 0.7082 (t) cc_final: 0.6427 (m)
REVERT: A  760 GLU cc_start: 0.7303 (tp30) cc_final: 0.6894 (tm-30)
REVERT: A  840 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7080 (tpt-90)
REVERT: A  849 MET cc_start: 0.7650 (pmm) cc_final: 0.7359 (pmm)
REVERT: A 1002 VAL cc_start: 0.8678 (m) cc_final: 0.8354 (p)
REVERT: A 1145 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.4535 (ttp)
REVERT: A 1205 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.5228 (mmm160)
  outliers start: 34
  outliers final: 24
  residues processed: 166
  average time/residue: 0.0989
  time to fit residues: 21.2129
Evaluate side-chains
  174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1109 THR
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Chi-restraints excluded: chain A residue 1205 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0050
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
A1009 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.180619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.157590 restraints weight = 10243.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.31
r_work: 0.3955 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6841  Z= 0.136
  Angle     :  0.602   9.738   9269  Z= 0.297
  Chirality :  0.041   0.358   1062
  Planarity :  0.004   0.034   1157
  Dihedral  :  3.908  16.296    910
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 28.85 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.30), residues: 827
  helix:  1.85 (0.22), residues: 539
  sheet: -0.54 (0.65), residues: 71
  loop : -1.25 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 764 
 TYR   0.017   0.001   TYR A 118 
 PHE   0.016   0.001   PHE A 780 
 TRP   0.016   0.001   TRP A 510 
 HIS   0.011   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6840)
  covalent geometry    : angle       0.60156 ( 9267)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       0.34108 (    2)
  hydrogen bonds       : bond        0.03668 (  458)
  hydrogen bonds       : angle       4.50149 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.2943 (OUTLIER) cc_final: 0.2221 (mm-30)
REVERT: A  146 VAL cc_start: 0.7506 (p) cc_final: 0.7234 (m)
REVERT: A  164 PHE cc_start: 0.7671 (m-80) cc_final: 0.7384 (m-80)
REVERT: A  193 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5767 (mp10)
REVERT: A  223 SER cc_start: 0.8200 (m) cc_final: 0.7894 (p)
REVERT: A  234 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8083 (tp)
REVERT: A  246 LEU cc_start: 0.8206 (tp) cc_final: 0.7998 (tt)
REVERT: A  326 GLU cc_start: 0.6917 (tt0) cc_final: 0.6251 (mt-10)
REVERT: A  387 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5990 (mtm)
REVERT: A  487 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7472 (mtp-110)
REVERT: A  760 GLU cc_start: 0.7338 (tp30) cc_final: 0.6897 (tm-30)
REVERT: A  773 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8173 (mmtm)
REVERT: A  840 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7092 (tpt-90)
REVERT: A  922 SER cc_start: 0.8214 (m) cc_final: 0.7868 (m)
REVERT: A 1002 VAL cc_start: 0.8665 (m) cc_final: 0.8337 (p)
REVERT: A 1145 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.4634 (ttp)
  outliers start: 33
  outliers final: 23
  residues processed: 159
  average time/residue: 0.1009
  time to fit residues: 20.8900
Evaluate side-chains
  170 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0000
   chunk 26 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.180230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.157271 restraints weight = 10234.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 2.29
r_work: 0.3960 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6841  Z= 0.140
  Angle     :  0.604   9.508   9269  Z= 0.301
  Chirality :  0.041   0.347   1062
  Planarity :  0.004   0.034   1157
  Dihedral  :  3.894  16.657    910
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 29.40 %
    Favored  : 66.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 827
  helix:  1.83 (0.22), residues: 539
  sheet: -0.41 (0.65), residues: 71
  loop : -1.23 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 764 
 TYR   0.016   0.001   TYR A 118 
 PHE   0.015   0.001   PHE A 780 
 TRP   0.016   0.001   TRP A 510 
 HIS   0.011   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6840)
  covalent geometry    : angle       0.60446 ( 9267)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.27163 (    2)
  hydrogen bonds       : bond        0.03638 (  458)
  hydrogen bonds       : angle       4.48959 ( 1389)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.3004 (OUTLIER) cc_final: 0.2258 (mm-30)
REVERT: A  106 GLU cc_start: 0.7198 (pp20) cc_final: 0.6720 (pp20)
REVERT: A  146 VAL cc_start: 0.7520 (p) cc_final: 0.7264 (m)
REVERT: A  164 PHE cc_start: 0.7655 (m-80) cc_final: 0.7376 (m-80)
REVERT: A  193 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5755 (mp10)
REVERT: A  223 SER cc_start: 0.8206 (m) cc_final: 0.7890 (p)
REVERT: A  234 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8074 (tp)
REVERT: A  326 GLU cc_start: 0.6916 (tt0) cc_final: 0.6192 (mt-10)
REVERT: A  387 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5997 (mtm)
REVERT: A  532 SER cc_start: 0.7102 (t) cc_final: 0.6490 (m)
REVERT: A  760 GLU cc_start: 0.7337 (tp30) cc_final: 0.6897 (tm-30)
REVERT: A  773 LYS cc_start: 0.8338 (mmtp) cc_final: 0.8129 (mmtm)
REVERT: A  849 MET cc_start: 0.7651 (pmm) cc_final: 0.7392 (pmm)
REVERT: A  922 SER cc_start: 0.8203 (m) cc_final: 0.7869 (m)
REVERT: A 1002 VAL cc_start: 0.8665 (m) cc_final: 0.8343 (p)
REVERT: A 1145 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.4589 (ttp)
  outliers start: 27
  outliers final: 22
  residues processed: 162
  average time/residue: 0.1083
  time to fit residues: 22.3705
Evaluate side-chains
  169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0570
   chunk 62 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.179521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.156524 restraints weight = 10064.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.28
r_work: 0.3953 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6841  Z= 0.153
  Angle     :  0.631   9.839   9269  Z= 0.312
  Chirality :  0.041   0.341   1062
  Planarity :  0.004   0.034   1157
  Dihedral  :  3.928  16.374    910
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.54 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.29), residues: 827
  helix:  1.78 (0.21), residues: 543
  sheet: -0.61 (0.66), residues: 71
  loop : -1.36 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 764 
 TYR   0.017   0.001   TYR A 118 
 PHE   0.015   0.001   PHE A 403 
 TRP   0.016   0.001   TRP A 510 
 HIS   0.011   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6840)
  covalent geometry    : angle       0.63108 ( 9267)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.28792 (    2)
  hydrogen bonds       : bond        0.03673 (  458)
  hydrogen bonds       : angle       4.51975 ( 1389)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1665.67 seconds
wall clock time: 29 minutes 25.27 seconds (1765.27 seconds total)