Starting phenix.real_space_refine
on Sat Aug 23 08:07:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dps_27641/08_2025/8dps_27641.map"
  }
  resolution = 3.47
  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=   0.000 sd=   1.000
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      36      5.16       5
     C    6752      2.51       5
     N    1826      2.21       5
     O    1996      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10610
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2382
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 280}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1262
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150}
    Chain: "C"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1566
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 25, 'TRANS': 174}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    D, E, F, I, J
  Time building chain proxies: 2.50, per 1000 atoms: 0.24
  Number of scatterers: 10610
  At special positions: 0
  Unit cell: (148.03, 129.69, 90.39, 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      36     16.00
     O    1996      8.00
     N    1826      7.00
     C    6752      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  81 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 150 " - pdb=" SG  CYS A 160 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  98 " - pdb=" SG  CYS C 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 148 " - pdb=" SG  CYS C 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  32 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  81 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 112 " - pdb=" SG  CYS D 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 150 " - pdb=" SG  CYS D 160 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F  98 " - pdb=" SG  CYS F 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 148 " - pdb=" SG  CYS F 158 " 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
      
  Atom "HETATM10499  O5  NAG I   1 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM10432  O5  NAG G   1 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM10580  O5  NAG A 402 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM10608  O5  NAG D 402 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM10566  O5  NAG A 401 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM10594  O5  NAG D 401 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
    NAG-ASN
      " NAG A 401 " - " ASN A  21 "
      " NAG A 402 " - " ASN A 135 "
      " NAG D 401 " - " ASN D  21 "
      " NAG D 402 " - " ASN D 135 "
      " NAG G   1 " - " ASN A  61 "
      " NAG H   1 " - " ASN C 172 "
      " NAG I   1 " - " ASN D  61 "
      " NAG J   1 " - " ASN F 172 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 388.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2504

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 24 sheets defined
      24.5% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 37
    Processing helix  chain 'A' and resid 39 through 41
      No H-bonds generated for 'chain 'A' and resid 39 through 41'
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 193 through 196
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.866A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 43
      removed outlier: 3.856A  pdb=" N   SER B  20 " --> pdb=" O   ALA B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
      removed outlier: 3.572A  pdb=" N   LEU B  64 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 65'
    Processing helix  chain 'B' and resid 68 through 94
      removed outlier: 3.746A  pdb=" N   VAL B  72 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B  92 " --> pdb=" O   GLN B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 102
      removed outlier: 4.394A  pdb=" N   THR B 100 " --> pdb=" O   SER B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 126
    Processing helix  chain 'B' and resid 145 through 157
    Processing helix  chain 'B' and resid 159 through 178
      removed outlier: 3.738A  pdb=" N   ASP B 165 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
    Processing helix  chain 'D' and resid 29 through 37
    Processing helix  chain 'D' and resid 39 through 41
      No H-bonds generated for 'chain 'D' and resid 39 through 41'
    Processing helix  chain 'D' and resid 53 through 55
      No H-bonds generated for 'chain 'D' and resid 53 through 55'
    Processing helix  chain 'D' and resid 193 through 196
    Processing helix  chain 'D' and resid 225 through 230
    Processing helix  chain 'D' and resid 251 through 256
      removed outlier: 3.865A  pdb=" N   ALA D 256 " --> pdb=" O   GLU D 253 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 43
      removed outlier: 3.855A  pdb=" N   SER E  20 " --> pdb=" O   ALA E  16 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 65
      removed outlier: 3.571A  pdb=" N   LEU E  64 " --> pdb=" O   ALA E  61 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY E  65 " --> pdb=" O   GLY E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 65'
    Processing helix  chain 'E' and resid 68 through 94
      removed outlier: 3.746A  pdb=" N   VAL E  72 " --> pdb=" O   GLN E  68 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU E  73 " --> pdb=" O   LEU E  69 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG E  92 " --> pdb=" O   GLN E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 102
      removed outlier: 4.393A  pdb=" N   THR E 100 " --> pdb=" O   SER E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 126
    Processing helix  chain 'E' and resid 145 through 157
    Processing helix  chain 'E' and resid 159 through 178
      removed outlier: 3.738A  pdb=" N   ASP E 165 " --> pdb=" O   HIS E 161 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG E 177 " --> pdb=" O   LEU E 173 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 190 through 194
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10
      removed outlier: 6.718A  pdb=" N   ALA A  64 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 5.622A  pdb=" N   ASN A  92 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ILE A  83 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161
      removed outlier: 4.190A  pdb=" N   ASP A 125 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   ASN A 109 " --> pdb=" O   ASP A 125 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   LYS A 199 " --> pdb=" O   CYS A 112 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   VAL A 114 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151
    Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 210
      removed outlier: 5.680A  pdb=" N   ASN A 205 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR A 223 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 248 through 249
    Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 99
    Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 147
    Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 147
    Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 206
      removed outlier: 4.137A  pdb=" N   LEU C 202 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   SER C 217 " --> pdb=" O   LEU C 202 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL C 204 " --> pdb=" O   ARG C 215 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ARG C 215 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 247 through 249
    Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 10
      removed outlier: 6.717A  pdb=" N   ALA D  64 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 17
      removed outlier: 5.621A  pdb=" N   ASN D  92 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE D  83 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161
      removed outlier: 4.191A  pdb=" N   ASP D 125 " --> pdb=" O   ASN D 109 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   ASN D 109 " --> pdb=" O   ASP D 125 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   LYS D 199 " --> pdb=" O   CYS D 112 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   VAL D 114 " --> pdb=" O   LYS D 199 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 150 through 151
    Processing sheet with id=AB8, first strand: chain 'D' and resid 150 through 151
    Processing sheet with id=AB9, first strand: chain 'D' and resid 204 through 210
      removed outlier: 5.681A  pdb=" N   ASN D 205 " --> pdb=" O   THR D 223 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR D 223 " --> pdb=" O   ASN D 205 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249
    Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 99
    Processing sheet with id=AC3, first strand: chain 'F' and resid 146 through 147
    Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147
    Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 206
      removed outlier: 4.138A  pdb=" N   LEU F 202 " --> pdb=" O   SER F 217 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   SER F 217 " --> pdb=" O   LEU F 202 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   VAL F 204 " --> pdb=" O   ARG F 215 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ARG F 215 " --> pdb=" O   VAL F 204 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 249

    492 hydrogen bonds defined for protein.
    1266 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: 1.60

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3405
        1.35 -     1.48: 2940
        1.48 -     1.61: 4513
        1.61 -     1.75: 2
        1.75 -     1.88: 44
  Bond restraints: 10904
  Sorted by residual:
  bond pdb=" CB  TRP A 142 "
       pdb=" CG  TRP A 142 "
    ideal  model  delta    sigma   weight residual
    1.498  1.404  0.094 3.10e-02 1.04e+03 9.10e+00
  bond pdb=" CB  TRP D 142 "
       pdb=" CG  TRP D 142 "
    ideal  model  delta    sigma   weight residual
    1.498  1.405  0.093 3.10e-02 1.04e+03 9.08e+00
  bond pdb=" CB  CYS A 160 "
       pdb=" SG  CYS A 160 "
    ideal  model  delta    sigma   weight residual
    1.808  1.879 -0.071 3.30e-02 9.18e+02 4.69e+00
  bond pdb=" CB  CYS D 160 "
       pdb=" SG  CYS D 160 "
    ideal  model  delta    sigma   weight residual
    1.808  1.878 -0.070 3.30e-02 9.18e+02 4.54e+00
  bond pdb=" CG  LEU C 186 "
       pdb=" CD2 LEU C 186 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.41e+00
  ... (remaining 10899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.52: 14696
        4.52 -     9.03: 178
        9.03 -    13.55: 18
       13.55 -    18.07: 8
       18.07 -    22.59: 2
  Bond angle restraints: 14902
  Sorted by residual:
  angle pdb=" C   ALA D 148 "
        pdb=" N   ASP D 149 "
        pdb=" CA  ASP D 149 "
      ideal   model   delta    sigma   weight residual
     120.94  132.46  -11.52 1.57e+00 4.06e-01 5.38e+01
  angle pdb=" C   ALA A 148 "
        pdb=" N   ASP A 149 "
        pdb=" CA  ASP A 149 "
      ideal   model   delta    sigma   weight residual
     120.94  132.42  -11.48 1.57e+00 4.06e-01 5.34e+01
  angle pdb=" CA  CYS A 150 "
        pdb=" CB  CYS A 150 "
        pdb=" SG  CYS A 150 "
      ideal   model   delta    sigma   weight residual
     114.40  129.32  -14.92 2.30e+00 1.89e-01 4.21e+01
  angle pdb=" CA  CYS D 150 "
        pdb=" CB  CYS D 150 "
        pdb=" SG  CYS D 150 "
      ideal   model   delta    sigma   weight residual
     114.40  129.31  -14.91 2.30e+00 1.89e-01 4.20e+01
  angle pdb=" CA  LEU E 173 "
        pdb=" CB  LEU E 173 "
        pdb=" CG  LEU E 173 "
      ideal   model   delta    sigma   weight residual
     116.30  138.89  -22.59 3.50e+00 8.16e-02 4.16e+01
  ... (remaining 14897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.09: 6180
       19.09 -    38.18: 450
       38.18 -    57.28: 76
       57.28 -    76.37: 40
       76.37 -    95.46: 10
  Dihedral angle restraints: 6756
    sinusoidal: 2892
      harmonic: 3864
  Sorted by residual:
  dihedral pdb=" CB  CYS A   6 "
           pdb=" SG  CYS A   6 "
           pdb=" SG  CYS A  32 "
           pdb=" CB  CYS A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.57   48.43     1      1.00e+01 1.00e-02 3.23e+01
  dihedral pdb=" CB  CYS D   6 "
           pdb=" SG  CYS D   6 "
           pdb=" SG  CYS D  32 "
           pdb=" CB  CYS D  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.60   48.40     1      1.00e+01 1.00e-02 3.23e+01
  dihedral pdb=" C   PHE A 147 "
           pdb=" N   PHE A 147 "
           pdb=" CA  PHE A 147 "
           pdb=" CB  PHE A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.89   13.29     0      2.50e+00 1.60e-01 2.83e+01
  ... (remaining 6753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.179: 1674
       0.179 -    0.359: 20
       0.359 -    0.538: 10
       0.538 -    0.717: 0
       0.717 -    0.897: 4
  Chirality restraints: 1708
  Sorted by residual:
  chirality pdb=" C1  NAG I   1 "
            pdb=" ND2 ASN D  61 "
            pdb=" C2  NAG I   1 "
            pdb=" O5  NAG I   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.50   -0.90 2.00e-01 2.50e+01 2.01e+01
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A  61 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.50   -0.90 2.00e-01 2.50e+01 2.00e+01
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN C 172 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.64   -0.76 2.00e-01 2.50e+01 1.45e+01
  ... (remaining 1705 not shown)

  Planarity restraints: 1894
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  61 "    0.240 2.00e-02 2.50e+03   3.09e-01 1.19e+03
        pdb=" CG  ASN A  61 "   -0.097 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  61 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  61 "   -0.494 2.00e-02 2.50e+03
        pdb=" C1  NAG G   1 "    0.403 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  61 "    0.240 2.00e-02 2.50e+03   3.08e-01 1.19e+03
        pdb=" CG  ASN D  61 "   -0.098 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  61 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  61 "   -0.494 2.00e-02 2.50e+03
        pdb=" C1  NAG I   1 "    0.402 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 172 "   -0.109 2.00e-02 2.50e+03   1.31e-01 2.15e+02
        pdb=" CG  ASN C 172 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 172 "    0.015 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 172 "    0.218 2.00e-02 2.50e+03
        pdb=" C1  NAG H   1 "   -0.158 2.00e-02 2.50e+03
  ... (remaining 1891 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 211
        2.63 -     3.20: 9855
        3.20 -     3.77: 16271
        3.77 -     4.33: 21793
        4.33 -     4.90: 36372
  Nonbonded interactions: 84502
  Sorted by model distance:
  nonbonded pdb=" O   THR A 144 "
            pdb=" ND1 HIS A 145 "
     model   vdw
     2.063 3.120
  nonbonded pdb=" O   THR D 144 "
            pdb=" ND1 HIS D 145 "
     model   vdw
     2.064 3.120
  nonbonded pdb=" OG1 THR A  58 "
            pdb=" OG  SER A  66 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" OG1 THR D  58 "
            pdb=" OG  SER D  66 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OG  SER A 261 "
            pdb=" OG  SER C 247 "
     model   vdw
     2.114 3.040
  ... (remaining 84497 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'H'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.640
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
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      :  0.008   0.094  10930  Z= 0.338
  Angle     :  1.820  49.774  14968  Z= 0.838
  Chirality :  0.081   0.897   1708
  Planarity :  0.006   0.050   1886
  Dihedral  : 14.649  95.461   4216
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.66 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  2.35 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.57 (0.21), residues: 1308
  helix:  1.10 (0.29), residues: 238
  sheet:  0.22 (0.23), residues: 420
  loop : -1.37 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.002   ARG C 121 
 TYR   0.021   0.004   TYR C  89 
 PHE   0.047   0.004   PHE F 230 
 TRP   0.042   0.004   TRP A  45 
 HIS   0.008   0.002   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00755 (10904)
  covalent geometry    : angle       1.40053 (14902)
  SS BOND              : bond        0.00839 (   12)
  SS BOND              : angle       3.73599 (   24)
  hydrogen bonds       : bond        0.23379 (  452)
  hydrogen bonds       : angle       8.03459 ( 1266)
  link_BETA1-4         : bond        0.00954 (    6)
  link_BETA1-4         : angle       2.55199 (   18)
  link_NAG-ASN         : bond        0.02228 (    8)
  link_NAG-ASN         : angle      28.79182 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 173
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7598 (t0)
REVERT: C   99 GLN cc_start: 0.5717 (pm20) cc_final: 0.5500 (pm20)
REVERT: C  105 ASN cc_start: 0.7783 (p0) cc_final: 0.7476 (p0)
REVERT: C  125 SER cc_start: 0.8145 (t) cc_final: 0.7579 (m)
REVERT: D   62 ARG cc_start: 0.7243 (mtp-110) cc_final: 0.7022 (ptp-110)
REVERT: D  109 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (t0)
REVERT: F   99 GLN cc_start: 0.5867 (pm20) cc_final: 0.5591 (pm20)
REVERT: F  256 GLU cc_start: 0.6659 (tp30) cc_final: 0.6332 (tp30)
  outliers start: 6
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0949
  time to fit residues: 24.4473
Evaluate side-chains
  123 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASN
Chi-restraints excluded: chain D residue  109 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 129 optimal weight:    2.9990
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
C 114 GLN
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.174902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.150444 restraints weight = 14385.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 2.51
r_work: 0.3867 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10930  Z= 0.185
  Angle     :  0.905  17.027  14968  Z= 0.426
  Chirality :  0.050   0.255   1708
  Planarity :  0.005   0.040   1886
  Dihedral  :  8.184  57.930   1736
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.22 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.18 (0.22), residues: 1308
  helix:  0.89 (0.30), residues: 264
  sheet:  0.53 (0.23), residues: 408
  loop : -0.42 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 154 
 TYR   0.024   0.002   TYR D 239 
 PHE   0.027   0.002   PHE F 106 
 TRP   0.016   0.002   TRP D 222 
 HIS   0.006   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10904)
  covalent geometry    : angle       0.85291 (14902)
  SS BOND              : bond        0.00467 (   12)
  SS BOND              : angle       2.14802 (   24)
  hydrogen bonds       : bond        0.05600 (  452)
  hydrogen bonds       : angle       6.06247 ( 1266)
  link_BETA1-4         : bond        0.00958 (    6)
  link_BETA1-4         : angle       2.35375 (   18)
  link_NAG-ASN         : bond        0.01315 (    8)
  link_NAG-ASN         : angle       7.12884 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 TYR cc_start: 0.6059 (t80) cc_final: 0.5821 (t80)
REVERT: A  109 ASN cc_start: 0.7916 (t0) cc_final: 0.7162 (t0)
REVERT: C  125 SER cc_start: 0.8280 (t) cc_final: 0.7962 (m)
REVERT: C  151 ASP cc_start: 0.5093 (OUTLIER) cc_final: 0.4455 (m-30)
REVERT: C  272 SER cc_start: 0.6526 (m) cc_final: 0.6270 (m)
REVERT: D   33 MET cc_start: 0.6398 (tmm) cc_final: 0.6164 (tmm)
REVERT: D  109 ASN cc_start: 0.7808 (t0) cc_final: 0.7001 (t0)
REVERT: E   56 THR cc_start: 0.8209 (t) cc_final: 0.7994 (t)
REVERT: F  256 GLU cc_start: 0.6861 (tp30) cc_final: 0.6359 (tp30)
  outliers start: 11
  outliers final: 6
  residues processed: 181
  average time/residue: 0.0968
  time to fit residues: 24.8214
Evaluate side-chains
  138 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0270
   chunk 67 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
C 114 GLN
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.173140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.148506 restraints weight = 14631.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.56
r_work: 0.3850 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10930  Z= 0.157
  Angle     :  0.765  15.725  14968  Z= 0.367
  Chirality :  0.047   0.275   1708
  Planarity :  0.005   0.042   1886
  Dihedral  :  6.758  57.903   1732
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.09 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.47 (0.23), residues: 1308
  helix:  1.15 (0.32), residues: 252
  sheet:  0.49 (0.23), residues: 412
  loop : -0.05 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  62 
 TYR   0.020   0.002   TYR D 239 
 PHE   0.025   0.002   PHE C 106 
 TRP   0.024   0.001   TRP D 222 
 HIS   0.004   0.001   HIS F 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10904)
  covalent geometry    : angle       0.73087 (14902)
  SS BOND              : bond        0.00709 (   12)
  SS BOND              : angle       1.71123 (   24)
  hydrogen bonds       : bond        0.04677 (  452)
  hydrogen bonds       : angle       5.79381 ( 1266)
  link_BETA1-4         : bond        0.00851 (    6)
  link_BETA1-4         : angle       2.26493 (   18)
  link_NAG-ASN         : bond        0.00807 (    8)
  link_NAG-ASN         : angle       5.15469 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8024 (t0) cc_final: 0.7256 (t0)
REVERT: A  177 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7428 (mt-10)
REVERT: B   42 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7768 (mtpp)
REVERT: C  114 GLN cc_start: 0.8282 (mt0) cc_final: 0.6523 (pp30)
REVERT: C  188 VAL cc_start: 0.8402 (t) cc_final: 0.8197 (t)
REVERT: C  256 GLU cc_start: 0.6755 (tp30) cc_final: 0.6233 (tp30)
REVERT: C  272 SER cc_start: 0.6702 (m) cc_final: 0.6457 (m)
REVERT: D  109 ASN cc_start: 0.7785 (t0) cc_final: 0.6964 (t0)
REVERT: D  296 SER cc_start: 0.7073 (m) cc_final: 0.6799 (p)
REVERT: E   56 THR cc_start: 0.8198 (t) cc_final: 0.7936 (t)
REVERT: F  188 VAL cc_start: 0.8464 (t) cc_final: 0.8201 (t)
REVERT: F  256 GLU cc_start: 0.6856 (tp30) cc_final: 0.6377 (tp30)
  outliers start: 24
  outliers final: 9
  residues processed: 163
  average time/residue: 0.0889
  time to fit residues: 20.9070
Evaluate side-chains
  131 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 86 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  86 HIS
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.166592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.141359 restraints weight = 14791.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.66
r_work: 0.3784 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  10930  Z= 0.200
  Angle     :  0.769  12.195  14968  Z= 0.371
  Chirality :  0.048   0.272   1708
  Planarity :  0.005   0.042   1886
  Dihedral  :  6.544  56.906   1732
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.04 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.08 (0.23), residues: 1308
  helix:  0.75 (0.33), residues: 264
  sheet:  0.02 (0.24), residues: 418
  loop : -0.08 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  62 
 TYR   0.024   0.002   TYR D  57 
 PHE   0.024   0.002   PHE C 106 
 TRP   0.032   0.002   TRP A 222 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (10904)
  covalent geometry    : angle       0.74435 (14902)
  SS BOND              : bond        0.00901 (   12)
  SS BOND              : angle       1.76882 (   24)
  hydrogen bonds       : bond        0.04466 (  452)
  hydrogen bonds       : angle       5.55269 ( 1266)
  link_BETA1-4         : bond        0.00857 (    6)
  link_BETA1-4         : angle       1.90573 (   18)
  link_NAG-ASN         : bond        0.00934 (    8)
  link_NAG-ASN         : angle       4.34482 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8009 (t0) cc_final: 0.6847 (t0)
REVERT: B   42 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7674 (mtpp)
REVERT: C  114 GLN cc_start: 0.8568 (mt0) cc_final: 0.8218 (mt0)
REVERT: C  188 VAL cc_start: 0.8391 (t) cc_final: 0.8148 (t)
REVERT: C  193 ILE cc_start: 0.8050 (tp) cc_final: 0.7835 (tt)
REVERT: C  256 GLU cc_start: 0.6743 (tp30) cc_final: 0.6172 (tp30)
REVERT: D   96 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7325 (pt)
REVERT: D  109 ASN cc_start: 0.7900 (t0) cc_final: 0.6676 (t0)
REVERT: E   42 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7683 (mtpp)
REVERT: E   56 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7713 (t)
REVERT: F  188 VAL cc_start: 0.8395 (t) cc_final: 0.8193 (t)
REVERT: F  256 GLU cc_start: 0.6689 (tp30) cc_final: 0.6349 (tp30)
  outliers start: 31
  outliers final: 22
  residues processed: 166
  average time/residue: 0.0875
  time to fit residues: 20.9204
Evaluate side-chains
  155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 125 optimal weight:    0.0670
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 93 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 145 HIS
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.170158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.145865 restraints weight = 14527.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.51
r_work: 0.3822 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10930  Z= 0.134
  Angle     :  0.696  14.136  14968  Z= 0.333
  Chirality :  0.045   0.285   1708
  Planarity :  0.004   0.040   1886
  Dihedral  :  6.086  57.399   1732
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.52 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.33 (0.24), residues: 1308
  helix:  1.08 (0.34), residues: 252
  sheet:  0.05 (0.24), residues: 422
  loop :  0.13 (0.27), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  93 
 TYR   0.016   0.001   TYR D 239 
 PHE   0.024   0.002   PHE C 230 
 TRP   0.025   0.001   TRP A 222 
 HIS   0.003   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10904)
  covalent geometry    : angle       0.67076 (14902)
  SS BOND              : bond        0.00296 (   12)
  SS BOND              : angle       1.62958 (   24)
  hydrogen bonds       : bond        0.03993 (  452)
  hydrogen bonds       : angle       5.37525 ( 1266)
  link_BETA1-4         : bond        0.00831 (    6)
  link_BETA1-4         : angle       1.78697 (   18)
  link_NAG-ASN         : bond        0.00497 (    8)
  link_NAG-ASN         : angle       4.20799 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8015 (t0) cc_final: 0.6874 (t0)
REVERT: B   42 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7575 (mtpp)
REVERT: C  188 VAL cc_start: 0.8456 (t) cc_final: 0.8175 (t)
REVERT: C  215 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7365 (ttt90)
REVERT: C  256 GLU cc_start: 0.6667 (tp30) cc_final: 0.6160 (tp30)
REVERT: E   42 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7617 (mtpp)
REVERT: E   56 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7644 (t)
REVERT: F  256 GLU cc_start: 0.6487 (tp30) cc_final: 0.6185 (tp30)
  outliers start: 28
  outliers final: 22
  residues processed: 171
  average time/residue: 0.1066
  time to fit residues: 26.0038
Evaluate side-chains
  154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 112 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0470
   chunk 49 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** 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 = 0.4193 r_free = 0.4193 target = 0.170254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.145664 restraints weight = 14565.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.47
r_work: 0.3827 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10930  Z= 0.143
  Angle     :  0.701  12.083  14968  Z= 0.335
  Chirality :  0.046   0.281   1708
  Planarity :  0.005   0.040   1886
  Dihedral  :  5.964  56.712   1732
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.61 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.23 (0.24), residues: 1308
  helix:  1.05 (0.34), residues: 250
  sheet: -0.05 (0.24), residues: 422
  loop :  0.09 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 128 
 TYR   0.016   0.002   TYR A   8 
 PHE   0.024   0.002   PHE C 230 
 TRP   0.027   0.002   TRP A 222 
 HIS   0.002   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10904)
  covalent geometry    : angle       0.67738 (14902)
  SS BOND              : bond        0.00538 (   12)
  SS BOND              : angle       1.64731 (   24)
  hydrogen bonds       : bond        0.03917 (  452)
  hydrogen bonds       : angle       5.30104 ( 1266)
  link_BETA1-4         : bond        0.00729 (    6)
  link_BETA1-4         : angle       1.74201 (   18)
  link_NAG-ASN         : bond        0.00790 (    8)
  link_NAG-ASN         : angle       4.06604 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 TYR cc_start: 0.5847 (t80) cc_final: 0.5640 (t80)
REVERT: A  109 ASN cc_start: 0.8009 (t0) cc_final: 0.6875 (t0)
REVERT: A  188 ASP cc_start: 0.7651 (m-30) cc_final: 0.7329 (t0)
REVERT: B   42 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7581 (mtpp)
REVERT: C  114 GLN cc_start: 0.8319 (mt0) cc_final: 0.8106 (mt0)
REVERT: C  215 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7362 (ttt90)
REVERT: C  256 GLU cc_start: 0.6567 (tp30) cc_final: 0.6079 (tp30)
REVERT: D   62 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7210 (ptm160)
REVERT: E   42 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7592 (mtpp)
REVERT: E   56 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7647 (t)
REVERT: F  256 GLU cc_start: 0.6413 (tp30) cc_final: 0.6106 (tp30)
  outliers start: 33
  outliers final: 24
  residues processed: 168
  average time/residue: 0.1061
  time to fit residues: 25.5498
Evaluate side-chains
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 112 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0870
   chunk 71 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0980
   chunk 74 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.6162

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

Flipped N/Q/H residues before XYZ refinement:
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** 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 = 0.4208 r_free = 0.4208 target = 0.171659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.146768 restraints weight = 14525.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.52
r_work: 0.3832 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10930  Z= 0.136
  Angle     :  0.693  11.575  14968  Z= 0.333
  Chirality :  0.045   0.259   1708
  Planarity :  0.004   0.038   1886
  Dihedral  :  5.880  56.837   1732
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.48 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.28 (0.24), residues: 1308
  helix:  1.13 (0.34), residues: 246
  sheet: -0.10 (0.24), residues: 416
  loop :  0.16 (0.27), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 128 
 TYR   0.016   0.001   TYR A   8 
 PHE   0.031   0.002   PHE F 230 
 TRP   0.024   0.002   TRP D 222 
 HIS   0.002   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10904)
  covalent geometry    : angle       0.66965 (14902)
  SS BOND              : bond        0.00297 (   12)
  SS BOND              : angle       1.61720 (   24)
  hydrogen bonds       : bond        0.03848 (  452)
  hydrogen bonds       : angle       5.25145 ( 1266)
  link_BETA1-4         : bond        0.00704 (    6)
  link_BETA1-4         : angle       1.65462 (   18)
  link_NAG-ASN         : bond        0.00601 (    8)
  link_NAG-ASN         : angle       4.10311 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8004 (t0) cc_final: 0.6869 (t0)
REVERT: B   42 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7484 (mtpp)
REVERT: C  215 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7392 (ttt90)
REVERT: C  256 GLU cc_start: 0.6499 (tp30) cc_final: 0.5819 (tp30)
REVERT: D   33 MET cc_start: 0.6916 (tmm) cc_final: 0.6642 (tmm)
REVERT: D   62 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7376 (ptm160)
REVERT: D  109 ASN cc_start: 0.7917 (t0) cc_final: 0.6693 (t0)
REVERT: E   42 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7508 (mtpp)
REVERT: E   56 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7660 (t)
REVERT: F  256 GLU cc_start: 0.6471 (tp30) cc_final: 0.6112 (tp30)
  outliers start: 29
  outliers final: 24
  residues processed: 167
  average time/residue: 0.1096
  time to fit residues: 26.0101
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.170988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.145983 restraints weight = 14553.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.54
r_work: 0.3821 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10930  Z= 0.156
  Angle     :  0.752  20.179  14968  Z= 0.353
  Chirality :  0.048   0.476   1708
  Planarity :  0.005   0.039   1886
  Dihedral  :  5.838  56.580   1732
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.48 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.17 (0.24), residues: 1308
  helix:  0.96 (0.34), residues: 246
  sheet: -0.18 (0.24), residues: 416
  loop :  0.15 (0.27), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 128 
 TYR   0.020   0.002   TYR F 122 
 PHE   0.030   0.002   PHE F 230 
 TRP   0.028   0.002   TRP A 222 
 HIS   0.002   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10904)
  covalent geometry    : angle       0.69954 (14902)
  SS BOND              : bond        0.00315 (   12)
  SS BOND              : angle       1.65313 (   24)
  hydrogen bonds       : bond        0.03906 (  452)
  hydrogen bonds       : angle       5.22135 ( 1266)
  link_BETA1-4         : bond        0.00663 (    6)
  link_BETA1-4         : angle       1.65797 (   18)
  link_NAG-ASN         : bond        0.00449 (    8)
  link_NAG-ASN         : angle       6.61705 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8021 (t0) cc_final: 0.6888 (t0)
REVERT: B  123 MET cc_start: 0.6340 (mmp) cc_final: 0.5529 (mmt)
REVERT: C  215 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7433 (ttt90)
REVERT: C  256 GLU cc_start: 0.6557 (tp30) cc_final: 0.5880 (tp30)
REVERT: D   62 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7380 (ttm-80)
REVERT: D  109 ASN cc_start: 0.7927 (t0) cc_final: 0.6705 (t0)
REVERT: E   56 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7692 (t)
REVERT: F  256 GLU cc_start: 0.6554 (tp30) cc_final: 0.6244 (tp30)
  outliers start: 30
  outliers final: 24
  residues processed: 155
  average time/residue: 0.1113
  time to fit residues: 24.4547
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  192 SER
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 120 optimal weight:    0.0070
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 118 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 ASN
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.172636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.147618 restraints weight = 14580.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.56
r_work: 0.3854 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10930  Z= 0.133
  Angle     :  0.687  11.220  14968  Z= 0.332
  Chirality :  0.045   0.254   1708
  Planarity :  0.004   0.037   1886
  Dihedral  :  5.782  56.640   1732
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.65 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.21 (0.24), residues: 1308
  helix:  1.03 (0.34), residues: 246
  sheet: -0.17 (0.24), residues: 416
  loop :  0.16 (0.27), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 128 
 TYR   0.016   0.001   TYR A   8 
 PHE   0.029   0.002   PHE C 230 
 TRP   0.025   0.002   TRP D 291 
 HIS   0.002   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10904)
  covalent geometry    : angle       0.66831 (14902)
  SS BOND              : bond        0.00314 (   12)
  SS BOND              : angle       1.60643 (   24)
  hydrogen bonds       : bond        0.03688 (  452)
  hydrogen bonds       : angle       5.16038 ( 1266)
  link_BETA1-4         : bond        0.00713 (    6)
  link_BETA1-4         : angle       1.56313 (   18)
  link_NAG-ASN         : bond        0.00428 (    8)
  link_NAG-ASN         : angle       3.59781 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.7967 (t0) cc_final: 0.6843 (t0)
REVERT: A  213 GLU cc_start: 0.7522 (mp0) cc_final: 0.7314 (mp0)
REVERT: B  123 MET cc_start: 0.6453 (mmp) cc_final: 0.5039 (mmt)
REVERT: C  215 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7451 (ttt90)
REVERT: C  256 GLU cc_start: 0.6479 (tp30) cc_final: 0.5810 (tp30)
REVERT: D   33 MET cc_start: 0.7030 (tmm) cc_final: 0.6764 (tmm)
REVERT: D   62 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7345 (ttm-80)
REVERT: D  109 ASN cc_start: 0.7895 (t0) cc_final: 0.6678 (t0)
REVERT: E   38 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8311 (tt0)
REVERT: E   56 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7695 (t)
REVERT: F  121 ARG cc_start: 0.6467 (ttp80) cc_final: 0.6152 (ttp-110)
REVERT: F  256 GLU cc_start: 0.6358 (tp30) cc_final: 0.6081 (tp30)
  outliers start: 29
  outliers final: 22
  residues processed: 162
  average time/residue: 0.1144
  time to fit residues: 26.1724
Evaluate side-chains
  152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   41 ASP
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  192 SER
Chi-restraints excluded: chain F residue  206 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0050
   chunk 90 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0870
   overall best weight:    0.5372

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.173313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.148180 restraints weight = 14502.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 2.56
r_work: 0.3847 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10930  Z= 0.133
  Angle     :  0.689  11.069  14968  Z= 0.332
  Chirality :  0.045   0.254   1708
  Planarity :  0.005   0.037   1886
  Dihedral  :  5.646  56.506   1732
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.17 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.17 (0.24), residues: 1308
  helix:  1.00 (0.34), residues: 246
  sheet: -0.19 (0.24), residues: 420
  loop :  0.14 (0.27), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 128 
 TYR   0.021   0.001   TYR F 122 
 PHE   0.031   0.002   PHE C 230 
 TRP   0.034   0.002   TRP F 282 
 HIS   0.002   0.000   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10904)
  covalent geometry    : angle       0.67631 (14902)
  SS BOND              : bond        0.00294 (   12)
  SS BOND              : angle       1.54696 (   24)
  hydrogen bonds       : bond        0.03633 (  452)
  hydrogen bonds       : angle       5.04794 ( 1266)
  link_BETA1-4         : bond        0.00800 (    6)
  link_BETA1-4         : angle       1.53168 (   18)
  link_NAG-ASN         : bond        0.00462 (    8)
  link_NAG-ASN         : angle       2.75625 (   24)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.7950 (t0) cc_final: 0.7136 (t0)
REVERT: B  123 MET cc_start: 0.6273 (mmp) cc_final: 0.4973 (mmt)
REVERT: C  122 TYR cc_start: 0.7288 (m-80) cc_final: 0.7076 (m-10)
REVERT: C  215 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7567 (ttt90)
REVERT: C  256 GLU cc_start: 0.6527 (tp30) cc_final: 0.5855 (tp30)
REVERT: D   33 MET cc_start: 0.6911 (tmm) cc_final: 0.6647 (tmm)
REVERT: D   62 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7412 (ttm-80)
REVERT: D  109 ASN cc_start: 0.7899 (t0) cc_final: 0.6684 (t0)
REVERT: F  121 ARG cc_start: 0.6437 (ttp80) cc_final: 0.6161 (ttp-110)
REVERT: F  256 GLU cc_start: 0.6404 (tp30) cc_final: 0.6099 (tp30)
REVERT: F  257 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.6712 (m)
  outliers start: 26
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1074
  time to fit residues: 24.1580
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  147 PHE
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  206 SER
Chi-restraints excluded: chain F residue  257 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 104 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0050
   chunk 129 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.173299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.148634 restraints weight = 14479.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 2.48
r_work: 0.3846 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10930  Z= 0.139
  Angle     :  0.695  11.100  14968  Z= 0.335
  Chirality :  0.045   0.275   1708
  Planarity :  0.004   0.037   1886
  Dihedral  :  5.599  56.395   1732
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.70 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.16 (0.24), residues: 1308
  helix:  1.01 (0.34), residues: 246
  sheet: -0.23 (0.24), residues: 420
  loop :  0.15 (0.27), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 118 
 TYR   0.018   0.002   TYR F 122 
 PHE   0.027   0.002   PHE F 230 
 TRP   0.035   0.002   TRP F 282 
 HIS   0.002   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10904)
  covalent geometry    : angle       0.68262 (14902)
  SS BOND              : bond        0.00304 (   12)
  SS BOND              : angle       1.64999 (   24)
  hydrogen bonds       : bond        0.03682 (  452)
  hydrogen bonds       : angle       5.05106 ( 1266)
  link_BETA1-4         : bond        0.00713 (    6)
  link_BETA1-4         : angle       1.52966 (   18)
  link_NAG-ASN         : bond        0.00400 (    8)
  link_NAG-ASN         : angle       2.76657 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2588.41 seconds
wall clock time: 45 minutes 17.59 seconds (2717.59 seconds total)