Starting phenix.real_space_refine
on Mon Sep 23 13:20:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owk_17239/09_2024/8owk_17239.cif"
  }
  resolution = 3.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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      10      5.16       5
     C    1940      2.51       5
     N     530      2.21       5
     O     570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 3050
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 305
          Classifications: {'peptide': 40}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.44, per 1000 atoms: 0.47
  Number of scatterers: 3050
  At special positions: 0
  Unit cell: (89.25, 120.75, 42, 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      10     16.00
     O     570      8.00
     N     530      7.00
     C    1940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 343.8 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 67.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 23
      removed outlier: 6.766A  pdb=" N   TYR C  10 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU B  11 " --> pdb=" O   TYR C  10 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL C  12 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   HIS B  13 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TYR A  10 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLU C  11 " --> pdb=" O   TYR A  10 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL A  12 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   HIS C  13 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   TYR D  10 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLU A  11 " --> pdb=" O   TYR D  10 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL D  12 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   HIS A  13 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU D   3 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   HIS E   6 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ARG D   5 " --> pdb=" O   HIS E   6 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   SER E   8 " --> pdb=" O   ARG D   5 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP D   7 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   TYR E  10 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLY D   9 " --> pdb=" O   TYR E  10 " (cutoff:3.500A)
      removed outlier: 10.199A  pdb=" N   VAL E  12 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   GLU D  11 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   HIS E  14 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   HIS D  13 " --> pdb=" O   HIS E  14 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LYS E  16 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   GLN D  15 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL E  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU D  17 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   PHE E  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE D  19 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   GLU E  22 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA D  21 " --> pdb=" O   GLU E  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36
      removed outlier: 6.876A  pdb=" N   ALA C  30 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ILE B  31 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE C  32 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY B  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 8.660A  pdb=" N   ALA A  30 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 9.741A  pdb=" N   GLY C  33 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE A  32 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   MET C  35 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU A  34 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ALA D  30 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE A  31 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE D  32 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   GLY A  33 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA E  30 " --> pdb=" O   GLY D  29 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE D  31 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE E  32 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLY D  33 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 23
      removed outlier: 6.766A  pdb=" N   TYR H  10 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU G  11 " --> pdb=" O   TYR H  10 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL H  12 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   HIS G  13 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   TYR F  10 " --> pdb=" O   GLY H   9 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLU H  11 " --> pdb=" O   TYR F  10 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL F  12 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   HIS H  13 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLU F   3 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   HIS I   6 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ARG F   5 " --> pdb=" O   HIS I   6 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   SER I   8 " --> pdb=" O   ARG F   5 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASP F   7 " --> pdb=" O   SER I   8 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   TYR I  10 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY F   9 " --> pdb=" O   TYR I  10 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   VAL I  12 " --> pdb=" O   GLY F   9 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   GLU F  11 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   HIS I  14 " --> pdb=" O   GLU F  11 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   HIS F  13 " --> pdb=" O   HIS I  14 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   LYS I  16 " --> pdb=" O   HIS F  13 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLN F  15 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   VAL I  18 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU F  17 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   PHE I  20 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   PHE F  19 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   GLU I  22 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA F  21 " --> pdb=" O   GLU I  22 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU I   3 " --> pdb=" O   PHE J   4 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   HIS J   6 " --> pdb=" O   GLU I   3 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ARG I   5 " --> pdb=" O   HIS J   6 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   SER J   8 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP I   7 " --> pdb=" O   SER J   8 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   TYR J  10 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLY I   9 " --> pdb=" O   TYR J  10 " (cutoff:3.500A)
      removed outlier: 10.199A  pdb=" N   VAL J  12 " --> pdb=" O   GLY I   9 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   GLU I  11 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   HIS J  14 " --> pdb=" O   GLU I  11 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   HIS I  13 " --> pdb=" O   HIS J  14 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LYS J  16 " --> pdb=" O   HIS I  13 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   GLN I  15 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL J  18 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU I  17 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   PHE J  20 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE I  19 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   GLU J  22 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA I  21 " --> pdb=" O   GLU J  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 29 through 36
      removed outlier: 6.876A  pdb=" N   ALA H  30 " --> pdb=" O   GLY G  29 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ILE G  31 " --> pdb=" O   ALA H  30 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE H  32 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY G  33 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   ALA F  30 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 9.777A  pdb=" N   GLY H  33 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE F  32 " --> pdb=" O   GLY H  33 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   MET H  35 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU F  34 " --> pdb=" O   MET H  35 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ALA I  30 " --> pdb=" O   GLY F  29 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE F  31 " --> pdb=" O   ALA I  30 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ILE I  32 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   GLY F  33 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA J  30 " --> pdb=" O   GLY I  29 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE I  31 " --> pdb=" O   ALA J  30 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE J  32 " --> pdb=" O   ILE I  31 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLY I  33 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    294 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: 0.71

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 950
        1.33 -     1.44: 492
        1.44 -     1.56: 1648
        1.56 -     1.67: 0
        1.67 -     1.79: 20
  Bond restraints: 3110
  Sorted by residual:
  bond pdb=" CA  HIS B   6 "
       pdb=" C   HIS B   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS G   6 "
       pdb=" C   HIS G   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS C   6 "
       pdb=" C   HIS C   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS H   6 "
       pdb=" C   HIS H   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS F   6 "
       pdb=" C   HIS F   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.43e+01
  ... (remaining 3105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.45: 4050
        6.45 -    12.90: 92
       12.90 -    19.35: 18
       19.35 -    25.80: 0
       25.80 -    32.25: 10
  Bond angle restraints: 4170
  Sorted by residual:
  angle pdb=" N   GLY I  25 "
        pdb=" CA  GLY I  25 "
        pdb=" C   GLY I  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY D  25 "
        pdb=" CA  GLY D  25 "
        pdb=" C   GLY D  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY A  25 "
        pdb=" CA  GLY A  25 "
        pdb=" C   GLY A  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY C  25 "
        pdb=" CA  GLY C  25 "
        pdb=" C   GLY C  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.60  -32.24 1.17e+00 7.31e-01 7.59e+02
  angle pdb=" N   GLY H  25 "
        pdb=" CA  GLY H  25 "
        pdb=" C   GLY H  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.60  -32.24 1.17e+00 7.31e-01 7.59e+02
  ... (remaining 4165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.42: 1425
        7.42 -    14.85: 285
       14.85 -    22.27: 10
       22.27 -    29.70: 10
       29.70 -    37.12: 10
  Dihedral angle restraints: 1740
    sinusoidal: 660
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" N   ILE E  32 "
           pdb=" C   ILE E  32 "
           pdb=" CA  ILE E  32 "
           pdb=" CB  ILE E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.41    7.99     0      2.50e+00 1.60e-01 1.02e+01
  dihedral pdb=" N   ILE J  32 "
           pdb=" C   ILE J  32 "
           pdb=" CA  ILE J  32 "
           pdb=" CB  ILE J  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.41    7.99     0      2.50e+00 1.60e-01 1.02e+01
  dihedral pdb=" N   ILE A  32 "
           pdb=" C   ILE A  32 "
           pdb=" CA  ILE A  32 "
           pdb=" CB  ILE A  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.46    7.94     0      2.50e+00 1.60e-01 1.01e+01
  ... (remaining 1737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.056: 150
       0.056 -    0.110: 125
       0.110 -    0.165: 95
       0.165 -    0.220: 30
       0.220 -    0.275: 40
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CG  LEU C  17 "
            pdb=" CB  LEU C  17 "
            pdb=" CD1 LEU C  17 "
            pdb=" CD2 LEU C  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CG  LEU H  17 "
            pdb=" CB  LEU H  17 "
            pdb=" CD1 LEU H  17 "
            pdb=" CD2 LEU H  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CG  LEU J  17 "
            pdb=" CB  LEU J  17 "
            pdb=" CD1 LEU J  17 "
            pdb=" CD2 LEU J  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 437 not shown)

  Planarity restraints: 550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  19 "    0.023 2.00e-02 2.50e+03   1.91e-02 6.41e+00
        pdb=" CG  PHE C  19 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  19 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  19 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  19 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  19 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  19 "   -0.023 2.00e-02 2.50e+03   1.91e-02 6.41e+00
        pdb=" CG  PHE H  19 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  19 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  19 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  19 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  19 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  19 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  19 "    0.023 2.00e-02 2.50e+03   1.90e-02 6.31e+00
        pdb=" CG  PHE A  19 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  19 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  19 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  19 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 547 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 1772
        2.99 -     3.47: 2833
        3.47 -     3.94: 5149
        3.94 -     4.42: 5764
        4.42 -     4.90: 11141
  Nonbonded interactions: 26659
  Sorted by model distance:
  nonbonded pdb=" O   ASP A   1 "
            pdb=" OE1 GLU A   3 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" O   ASP F   1 "
            pdb=" OE1 GLU F   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP C   1 "
            pdb=" OE1 GLU C   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP H   1 "
            pdb=" OE1 GLU H   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP J   1 "
            pdb=" OE1 GLU J   3 "
     model   vdw
     2.510 3.040
  ... (remaining 26654 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 group one per residue
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:             0.720
  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:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.750
  Find NCS groups from input model:        0.110
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
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      :  0.013   0.045   3110  Z= 0.855
  Angle     :  3.090  32.249   4170  Z= 2.193
  Chirality :  0.121   0.275    440
  Planarity :  0.008   0.022    550
  Dihedral  :  7.402  37.119   1060
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  6.45 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.43), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.58 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.005   HIS G   6 
 PHE   0.039   0.012   PHE C  19 
 TYR   0.042   0.010   TYR G  10 
 ARG   0.002   0.001   ARG C   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.5564 (mp0) cc_final: 0.4830 (tm-30)
REVERT: B   16 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7043 (ttpt)
REVERT: E   19 PHE cc_start: 0.7706 (m-80) cc_final: 0.7343 (m-80)
REVERT: G    3 GLU cc_start: 0.5571 (mp0) cc_final: 0.4837 (tm-30)
REVERT: G   16 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7049 (ttpt)
REVERT: J   19 PHE cc_start: 0.7700 (m-80) cc_final: 0.7336 (m-80)
REVERT: J   23 ASP cc_start: 0.6333 (t0) cc_final: 0.6126 (t0)
  outliers start: 10
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1474
  time to fit residues: 26.0828
Evaluate side-chains
  99 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain G residue   16 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
C   6 HIS
D   6 HIS
E   6 HIS
F   6 HIS
H   6 HIS
I   6 HIS
J   6 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3110  Z= 0.267
  Angle     :  0.809   7.978   4170  Z= 0.415
  Chirality :  0.054   0.159    440
  Planarity :  0.003   0.014    550
  Dihedral  :  6.692  19.433    418
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.90 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.36), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS G  14 
 PHE   0.013   0.003   PHE D  19 
 TYR   0.016   0.003   TYR F  10 
 ARG   0.003   0.001   ARG J   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1281
  time to fit residues: 16.5761
Evaluate side-chains
  70 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 36 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
F   6 HIS
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.035   3110  Z= 0.547
  Angle     :  0.829   8.458   4170  Z= 0.451
  Chirality :  0.059   0.205    440
  Planarity :  0.005   0.026    550
  Dihedral  :  6.447  19.003    410
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 10.00 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.005   HIS I  13 
 PHE   0.015   0.003   PHE E   4 
 TYR   0.017   0.004   TYR H  10 
 ARG   0.009   0.002   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1105
  time to fit residues: 11.6899
Evaluate side-chains
  76 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   16 LYS
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0370
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    5.4066

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 HIS
E   6 HIS
F   6 HIS
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 HIS
J   6 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.5517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.025   3110  Z= 0.427
  Angle     :  0.736   9.153   4170  Z= 0.383
  Chirality :  0.054   0.144    440
  Planarity :  0.004   0.025    550
  Dihedral  :  5.785  15.015    410
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 20.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.23 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.004   HIS D  13 
 PHE   0.010   0.002   PHE F  19 
 TYR   0.013   0.002   TYR I  10 
 ARG   0.005   0.001   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0953
  time to fit residues: 10.2084
Evaluate side-chains
  73 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
F   6 HIS
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.5870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.030   3110  Z= 0.463
  Angle     :  0.728   8.318   4170  Z= 0.392
  Chirality :  0.054   0.141    440
  Planarity :  0.004   0.024    550
  Dihedral  :  5.687  13.583    410
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.48 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.28), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.004   HIS J  13 
 PHE   0.011   0.003   PHE F  19 
 TYR   0.011   0.002   TYR I  10 
 ARG   0.005   0.001   ARG D   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0905
  time to fit residues: 9.0593
Evaluate side-chains
  77 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   31 ILE
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
F   6 HIS
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.6035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3110  Z= 0.367
  Angle     :  0.684   7.652   4170  Z= 0.362
  Chirality :  0.053   0.146    440
  Planarity :  0.003   0.023    550
  Dihedral  :  5.419  12.380    410
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 14.52 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.28), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS I  13 
 PHE   0.010   0.002   PHE F  19 
 TYR   0.009   0.002   TYR I  10 
 ARG   0.003   0.001   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0975
  time to fit residues: 9.7546
Evaluate side-chains
  74 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   31 ILE
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    0.3980
   chunk 17 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0170
   overall best weight:    3.2422

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.6161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3110  Z= 0.278
  Angle     :  0.634   7.175   4170  Z= 0.331
  Chirality :  0.052   0.147    440
  Planarity :  0.002   0.015    550
  Dihedral  :  5.102  12.487    410
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.84 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS I  13 
 PHE   0.009   0.002   PHE F  19 
 TYR   0.006   0.001   TYR I  10 
 ARG   0.003   0.001   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.5831 (mp0) cc_final: 0.5164 (tm-30)
REVERT: C    3 GLU cc_start: 0.5335 (mp0) cc_final: 0.4967 (tm-30)
REVERT: E    5 ARG cc_start: 0.7783 (ttm110) cc_final: 0.6771 (tmm160)
REVERT: G    3 GLU cc_start: 0.5893 (mp0) cc_final: 0.5191 (tm-30)
REVERT: H    3 GLU cc_start: 0.5377 (mp0) cc_final: 0.4972 (tm-30)
REVERT: J    5 ARG cc_start: 0.7884 (ttm110) cc_final: 0.6777 (tmm160)
  outliers start: 8
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1184
  time to fit residues: 12.7436
Evaluate side-chains
  78 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.0970
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0370
   chunk 28 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.8262

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.6273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3110  Z= 0.190
  Angle     :  0.599   6.548   4170  Z= 0.307
  Chirality :  0.052   0.141    440
  Planarity :  0.002   0.008    550
  Dihedral  :  4.667  12.812    410
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.13 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  13 
 PHE   0.019   0.002   PHE J  20 
 TYR   0.006   0.001   TYR I  10 
 ARG   0.003   0.001   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.6099 (mp0) cc_final: 0.5454 (tm-30)
REVERT: C    3 GLU cc_start: 0.5425 (mp0) cc_final: 0.5088 (tm-30)
REVERT: E    5 ARG cc_start: 0.7745 (ttm110) cc_final: 0.6815 (tmm160)
REVERT: G    3 GLU cc_start: 0.6135 (mp0) cc_final: 0.5470 (tm-30)
REVERT: H    3 GLU cc_start: 0.5469 (mp0) cc_final: 0.5088 (tm-30)
REVERT: J    5 ARG cc_start: 0.7820 (ttm110) cc_final: 0.6784 (tmm160)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 0.1611
  time to fit residues: 15.6277
Evaluate side-chains
  74 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0770
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.9342

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.6452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3110  Z= 0.200
  Angle     :  0.608   6.554   4170  Z= 0.315
  Chirality :  0.052   0.143    440
  Planarity :  0.003   0.045    550
  Dihedral  :  4.667  14.073    410
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 17.10 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  13 
 PHE   0.019   0.002   PHE E  20 
 TYR   0.005   0.001   TYR D  10 
 ARG   0.012   0.002   ARG D   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.6077 (mp0) cc_final: 0.5539 (tm-30)
REVERT: C    3 GLU cc_start: 0.5421 (mp0) cc_final: 0.5100 (tm-30)
REVERT: E    5 ARG cc_start: 0.7876 (ttm110) cc_final: 0.6846 (tmm160)
REVERT: G    3 GLU cc_start: 0.6116 (mp0) cc_final: 0.5555 (tm-30)
REVERT: H    3 GLU cc_start: 0.5486 (mp0) cc_final: 0.5108 (tm-30)
REVERT: J    5 ARG cc_start: 0.7895 (ttm110) cc_final: 0.6830 (tmm160)
  outliers start: 2
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1325
  time to fit residues: 12.5364
Evaluate side-chains
  75 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.6554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3110  Z= 0.352
  Angle     :  0.664   6.669   4170  Z= 0.357
  Chirality :  0.053   0.142    440
  Planarity :  0.003   0.035    550
  Dihedral  :  5.115  15.675    410
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 17.42 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS H  13 
 PHE   0.017   0.002   PHE E  20 
 TYR   0.005   0.001   TYR D  10 
 ARG   0.012   0.002   ARG D   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B    3 GLU cc_start: 0.5759 (mp0) cc_final: 0.5129 (tm-30)
REVERT: C    3 GLU cc_start: 0.5306 (mp0) cc_final: 0.5039 (tm-30)
REVERT: E    5 ARG cc_start: 0.7963 (ttm110) cc_final: 0.6885 (tmm160)
REVERT: G    3 GLU cc_start: 0.5803 (mp0) cc_final: 0.5149 (tm-30)
REVERT: H    3 GLU cc_start: 0.5412 (mp0) cc_final: 0.5106 (tm-30)
REVERT: J    5 ARG cc_start: 0.8032 (ttm110) cc_final: 0.6896 (tmm160)
  outliers start: 2
  outliers final: 2
  residues processed: 83
  average time/residue: 0.1303
  time to fit residues: 13.3798
Evaluate side-chains
  80 residues out of total 310 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0470
   chunk 21 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 15 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    4.6086

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.093377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.073716 restraints weight = 6171.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.075411 restraints weight = 2685.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.076362 restraints weight = 1820.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.6694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3110  Z= 0.372
  Angle     :  0.688   6.806   4170  Z= 0.374
  Chirality :  0.055   0.153    440
  Planarity :  0.003   0.033    550
  Dihedral  :  5.281  16.754    410
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 18.71 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS D  13 
 PHE   0.017   0.002   PHE E  20 
 TYR   0.009   0.002   TYR J  10 
 ARG   0.012   0.001   ARG D   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 967.51 seconds
wall clock time: 17 minutes 44.56 seconds (1064.56 seconds total)