Starting phenix.real_space_refine
on Fri Sep 19 03:02:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g2r_50981/09_2025/9g2r_50981.map"
  }
  resolution = 3.88
  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=   0.021
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      96      5.16       5
     C   14160      2.51       5
     N    3988      2.21       5
     O    4376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22620
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1939
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "F"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1899
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1939
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "H"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1899
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1939
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "J"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1899
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1939
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "L"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1899
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
  Time building chain proxies: 5.95, per 1000 atoms: 0.26
  Number of scatterers: 22620
  At special positions: 0
  Unit cell: (148.736, 147.408, 171.312, 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      96     16.00
     O    4376      8.00
     N    3988      7.00
     C   14160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 948.1 milliseconds
  
  Enol-peptide restraints added in 1.9 microseconds
  

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5392

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 0 sheets defined
      93.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 31
      removed outlier: 3.851A  pdb=" N   ALA A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 68
    Processing helix  chain 'A' and resid 70 through 76
    Processing helix  chain 'A' and resid 92 through 109
    Processing helix  chain 'A' and resid 112 through 143
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.688A  pdb=" N   ILE A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 181
    Processing helix  chain 'A' and resid 184 through 252
      removed outlier: 3.864A  pdb=" N   ILE A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   SER A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   SER A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 31
    Processing helix  chain 'B' and resid 39 through 68
    Processing helix  chain 'B' and resid 70 through 76
    Processing helix  chain 'B' and resid 92 through 109
    Processing helix  chain 'B' and resid 112 through 143
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 153 through 182
    Processing helix  chain 'B' and resid 184 through 252
      removed outlier: 3.820A  pdb=" N   ILE B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 31
    Processing helix  chain 'C' and resid 39 through 68
    Processing helix  chain 'C' and resid 70 through 76
    Processing helix  chain 'C' and resid 92 through 109
    Processing helix  chain 'C' and resid 112 through 143
    Processing helix  chain 'C' and resid 143 through 154
      removed outlier: 3.688A  pdb=" N   ILE C 151 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 181
    Processing helix  chain 'C' and resid 184 through 252
      removed outlier: 3.864A  pdb=" N   ILE C 216 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   SER C 217 " --> pdb=" O   LEU C 213 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   SER C 218 " --> pdb=" O   GLU C 214 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR C 219 " --> pdb=" O   GLY C 215 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 31
    Processing helix  chain 'D' and resid 39 through 68
    Processing helix  chain 'D' and resid 70 through 76
    Processing helix  chain 'D' and resid 92 through 109
    Processing helix  chain 'D' and resid 112 through 143
    Processing helix  chain 'D' and resid 143 through 153
    Processing helix  chain 'D' and resid 153 through 182
    Processing helix  chain 'D' and resid 184 through 252
      removed outlier: 3.820A  pdb=" N   ILE D 216 " --> pdb=" O   LEU D 212 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   SER D 217 " --> pdb=" O   LEU D 213 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   SER D 218 " --> pdb=" O   GLU D 214 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 12 through 30
    Processing helix  chain 'E' and resid 39 through 68
    Processing helix  chain 'E' and resid 70 through 84
      removed outlier: 3.578A  pdb=" N   ARG E  74 " --> pdb=" O   ASN E  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 109
    Processing helix  chain 'E' and resid 112 through 143
    Processing helix  chain 'E' and resid 143 through 181
      removed outlier: 4.107A  pdb=" N   TYR E 155 " --> pdb=" O   ILE E 151 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LYS E 156 " --> pdb=" O   GLU E 152 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 184 through 215
      removed outlier: 3.972A  pdb=" N   GLY E 215 " --> pdb=" O   LEU E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 215 through 252
      removed outlier: 3.884A  pdb=" N   THR E 219 " --> pdb=" O   GLY E 215 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   HIS E 220 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 30
    Processing helix  chain 'F' and resid 39 through 68
    Processing helix  chain 'F' and resid 70 through 84
      removed outlier: 3.520A  pdb=" N   ARG F  74 " --> pdb=" O   ASN F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 109
    Processing helix  chain 'F' and resid 112 through 143
    Processing helix  chain 'F' and resid 143 through 153
      removed outlier: 3.529A  pdb=" N   LEU F 147 " --> pdb=" O   PHE F 143 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 153 through 181
      removed outlier: 3.541A  pdb=" N   THR F 157 " --> pdb=" O   GLY F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 184 through 215
    Processing helix  chain 'F' and resid 215 through 252
    Processing helix  chain 'G' and resid 12 through 30
    Processing helix  chain 'G' and resid 39 through 68
    Processing helix  chain 'G' and resid 70 through 84
      removed outlier: 3.579A  pdb=" N   ARG G  74 " --> pdb=" O   ASN G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 109
    Processing helix  chain 'G' and resid 112 through 143
    Processing helix  chain 'G' and resid 143 through 181
      removed outlier: 4.107A  pdb=" N   TYR G 155 " --> pdb=" O   ILE G 151 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LYS G 156 " --> pdb=" O   GLU G 152 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 184 through 215
      removed outlier: 3.971A  pdb=" N   GLY G 215 " --> pdb=" O   LEU G 211 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 215 through 252
      removed outlier: 3.884A  pdb=" N   THR G 219 " --> pdb=" O   GLY G 215 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   HIS G 220 " --> pdb=" O   ILE G 216 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA G 221 " --> pdb=" O   SER G 217 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 14 through 30
    Processing helix  chain 'H' and resid 39 through 68
    Processing helix  chain 'H' and resid 70 through 84
      removed outlier: 3.519A  pdb=" N   ARG H  74 " --> pdb=" O   ASN H  70 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 109
    Processing helix  chain 'H' and resid 112 through 143
    Processing helix  chain 'H' and resid 143 through 153
      removed outlier: 3.529A  pdb=" N   LEU H 147 " --> pdb=" O   PHE H 143 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 153 through 181
      removed outlier: 3.541A  pdb=" N   THR H 157 " --> pdb=" O   GLY H 153 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 184 through 215
    Processing helix  chain 'H' and resid 215 through 252
    Processing helix  chain 'I' and resid 12 through 30
    Processing helix  chain 'I' and resid 39 through 68
    Processing helix  chain 'I' and resid 70 through 83
      removed outlier: 3.579A  pdb=" N   ARG I  74 " --> pdb=" O   ASN I  70 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 92 through 109
    Processing helix  chain 'I' and resid 112 through 143
    Processing helix  chain 'I' and resid 143 through 181
      removed outlier: 4.107A  pdb=" N   TYR I 155 " --> pdb=" O   ILE I 151 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LYS I 156 " --> pdb=" O   GLU I 152 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 184 through 215
      removed outlier: 3.972A  pdb=" N   GLY I 215 " --> pdb=" O   LEU I 211 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 215 through 252
      removed outlier: 3.884A  pdb=" N   THR I 219 " --> pdb=" O   GLY I 215 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   HIS I 220 " --> pdb=" O   ILE I 216 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA I 221 " --> pdb=" O   SER I 217 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 14 through 30
    Processing helix  chain 'J' and resid 39 through 68
    Processing helix  chain 'J' and resid 70 through 84
      removed outlier: 3.520A  pdb=" N   ARG J  74 " --> pdb=" O   ASN J  70 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 109
    Processing helix  chain 'J' and resid 112 through 143
    Processing helix  chain 'J' and resid 143 through 153
      removed outlier: 3.529A  pdb=" N   LEU J 147 " --> pdb=" O   PHE J 143 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 153 through 181
      removed outlier: 3.541A  pdb=" N   THR J 157 " --> pdb=" O   GLY J 153 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 184 through 215
    Processing helix  chain 'J' and resid 215 through 252
    Processing helix  chain 'K' and resid 12 through 30
    Processing helix  chain 'K' and resid 39 through 68
    Processing helix  chain 'K' and resid 70 through 84
      removed outlier: 3.579A  pdb=" N   ARG K  74 " --> pdb=" O   ASN K  70 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 92 through 109
    Processing helix  chain 'K' and resid 112 through 143
    Processing helix  chain 'K' and resid 143 through 181
      removed outlier: 4.107A  pdb=" N   TYR K 155 " --> pdb=" O   ILE K 151 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LYS K 156 " --> pdb=" O   GLU K 152 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 184 through 215
      removed outlier: 3.971A  pdb=" N   GLY K 215 " --> pdb=" O   LEU K 211 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 215 through 252
      removed outlier: 3.884A  pdb=" N   THR K 219 " --> pdb=" O   GLY K 215 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   HIS K 220 " --> pdb=" O   ILE K 216 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ALA K 221 " --> pdb=" O   SER K 217 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 14 through 30
    Processing helix  chain 'L' and resid 39 through 68
    Processing helix  chain 'L' and resid 70 through 84
      removed outlier: 3.520A  pdb=" N   ARG L  74 " --> pdb=" O   ASN L  70 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 109
    Processing helix  chain 'L' and resid 112 through 143
    Processing helix  chain 'L' and resid 143 through 153
      removed outlier: 3.528A  pdb=" N   LEU L 147 " --> pdb=" O   PHE L 143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 153 through 181
      removed outlier: 3.541A  pdb=" N   THR L 157 " --> pdb=" O   GLY L 153 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 215
    Processing helix  chain 'L' and resid 215 through 252

    2185 hydrogen bonds defined for protein.
    6555 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: 4.09

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4925
        1.33 -     1.45: 4571
        1.45 -     1.57: 13284
        1.57 -     1.69: 0
        1.69 -     1.81: 144
  Bond restraints: 22924
  Sorted by residual:
  bond pdb=" N   THR C 145 "
       pdb=" CA  THR C 145 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 7.70e-03 1.69e+04 1.24e+01
  bond pdb=" N   THR A 145 "
       pdb=" CA  THR A 145 "
    ideal  model  delta    sigma   weight residual
    1.462  1.488 -0.026 7.70e-03 1.69e+04 1.15e+01
  bond pdb=" N   ILE K  91 "
       pdb=" CA  ILE K  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.035 1.20e-02 6.94e+03 8.62e+00
  bond pdb=" N   ASN D  93 "
       pdb=" CA  ASN D  93 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.027 9.20e-03 1.18e+04 8.54e+00
  bond pdb=" N   ASN B  93 "
       pdb=" CA  ASN B  93 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.027 9.20e-03 1.18e+04 8.53e+00
  ... (remaining 22919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 21067
        1.05 -     2.10: 5003
        2.10 -     3.15: 4529
        3.15 -     4.20: 197
        4.20 -     5.25: 48
  Bond angle restraints: 30844
  Sorted by residual:
  angle pdb=" N   LEU G  30 "
        pdb=" CA  LEU G  30 "
        pdb=" C   LEU G  30 "
      ideal   model   delta    sigma   weight residual
     112.87  108.06    4.81 1.20e+00 6.94e-01 1.61e+01
  angle pdb=" N   LEU I  30 "
        pdb=" CA  LEU I  30 "
        pdb=" C   LEU I  30 "
      ideal   model   delta    sigma   weight residual
     112.87  108.07    4.80 1.20e+00 6.94e-01 1.60e+01
  angle pdb=" N   LEU K  30 "
        pdb=" CA  LEU K  30 "
        pdb=" C   LEU K  30 "
      ideal   model   delta    sigma   weight residual
     112.87  108.08    4.79 1.20e+00 6.94e-01 1.59e+01
  angle pdb=" N   LEU E  30 "
        pdb=" CA  LEU E  30 "
        pdb=" C   LEU E  30 "
      ideal   model   delta    sigma   weight residual
     112.87  108.08    4.79 1.20e+00 6.94e-01 1.59e+01
  angle pdb=" N   GLY G  31 "
        pdb=" CA  GLY G  31 "
        pdb=" C   GLY G  31 "
      ideal   model   delta    sigma   weight residual
     115.40  110.26    5.14 1.32e+00 5.74e-01 1.52e+01
  ... (remaining 30839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.51: 12861
       15.51 -    31.01: 961
       31.01 -    46.52: 223
       46.52 -    62.02: 165
       62.02 -    77.53: 30
  Dihedral angle restraints: 14240
    sinusoidal: 5952
      harmonic: 8288
  Sorted by residual:
  dihedral pdb=" CD  ARG H 210 "
           pdb=" NE  ARG H 210 "
           pdb=" CZ  ARG H 210 "
           pdb=" NH1 ARG H 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.72  -32.72     1      1.00e+01 1.00e-02 1.52e+01
  dihedral pdb=" CD  ARG L 210 "
           pdb=" NE  ARG L 210 "
           pdb=" CZ  ARG L 210 "
           pdb=" NH1 ARG L 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.61  -32.61     1      1.00e+01 1.00e-02 1.51e+01
  dihedral pdb=" CD  ARG F 210 "
           pdb=" NE  ARG F 210 "
           pdb=" CZ  ARG F 210 "
           pdb=" NH1 ARG F 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.61  -32.61     1      1.00e+01 1.00e-02 1.51e+01
  ... (remaining 14237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1344
       0.044 -    0.088: 779
       0.088 -    0.132: 813
       0.132 -    0.176: 440
       0.176 -    0.220: 112
  Chirality restraints: 3488
  Sorted by residual:
  chirality pdb=" CA  ILE A  75 "
            pdb=" N   ILE A  75 "
            pdb=" C   ILE A  75 "
            pdb=" CB  ILE A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE C  75 "
            pdb=" N   ILE C  75 "
            pdb=" C   ILE C  75 "
            pdb=" CB  ILE C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE A 208 "
            pdb=" N   ILE A 208 "
            pdb=" C   ILE A 208 "
            pdb=" CB  ILE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 3485 not shown)

  Planarity restraints: 4012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 210 "   -0.574 9.50e-02 1.11e+02   2.57e-01 4.05e+01
        pdb=" NE  ARG H 210 "    0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 210 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 210 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 210 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 210 "    0.574 9.50e-02 1.11e+02   2.57e-01 4.05e+01
        pdb=" NE  ARG L 210 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 210 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 210 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 210 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 210 "   -0.574 9.50e-02 1.11e+02   2.57e-01 4.04e+01
        pdb=" NE  ARG F 210 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 210 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 210 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 210 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 4009 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 8339
        2.86 -     3.37: 26375
        3.37 -     3.88: 39049
        3.88 -     4.39: 44756
        4.39 -     4.90: 67443
  Nonbonded interactions: 185962
  Sorted by model distance:
  nonbonded pdb=" O   SER J 200 "
            pdb=" OD1 ASP J 203 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   SER F 200 "
            pdb=" OD1 ASP F 203 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   SER H 200 "
            pdb=" OD1 ASP H 203 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   SER L 200 "
            pdb=" OD1 ASP L 203 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" NE2 GLN K 243 "
            pdb=" OD1 ASP K 247 "
     model   vdw
     2.399 3.120
  ... (remaining 185957 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 13 through 30 or resid 35 through 252))
  selection = (chain 'B' and (resid 13 through 30 or resid 35 through 252))
  selection = (chain 'C' and (resid 13 through 30 or resid 35 through 252))
  selection = (chain 'D' and (resid 13 through 30 or resid 35 through 252))
  selection = (chain 'E' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 
52))
  selection = (chain 'F' and (resid 13 through 76 or resid 91 through 252))
  selection = (chain 'G' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 
52))
  selection = (chain 'H' and (resid 13 through 76 or resid 91 through 252))
  selection = (chain 'I' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 
52))
  selection = (chain 'J' and (resid 13 through 76 or resid 91 through 252))
  selection = (chain 'K' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 
52))
  selection = (chain 'L' and (resid 13 through 76 or resid 91 through 252))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.240
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.060
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.010   0.045  22924  Z= 0.755
  Angle     :  1.235   5.251  30844  Z= 1.038
  Chirality :  0.090   0.220   3488
  Planarity :  0.023   0.257   4012
  Dihedral  : 13.902  77.527   8848
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.01 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.14), residues: 2784
  helix:  0.42 (0.09), residues: 2548
  sheet:  None (None), residues: 0
  loop : -2.11 (0.31), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.003   ARG E 127 
 TYR   0.024   0.002   TYR K 244 
 PHE   0.028   0.002   PHE L  78 
 TRP   0.006   0.001   TRP K  55 
 HIS   0.007   0.001   HIS J  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00967 (22924)
  covalent geometry    : angle       1.23505 (30844)
  hydrogen bonds       : bond        0.16674 ( 2185)
  hydrogen bonds       : angle       6.37205 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 250
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   60 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8700 (ppp)
REVERT: H  101 MET cc_start: 0.8822 (mtt) cc_final: 0.8449 (mtm)
REVERT: H  237 TYR cc_start: 0.8162 (t80) cc_final: 0.7816 (t80)
REVERT: I  132 ASP cc_start: 0.8108 (t0) cc_final: 0.7508 (t0)
  outliers start: 14
  outliers final: 1
  residues processed: 260
  average time/residue: 0.1608
  time to fit residues: 65.2945
Evaluate side-chains
  106 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   60 MET
Chi-restraints excluded: chain L residue   60 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 197 optimal weight:    8.9990
   chunk 215 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 132 optimal weight:    5.9990
   chunk 261 optimal weight:    9.9990
   chunk 248 optimal weight:    9.9990
   chunk 207 optimal weight:    0.0970
   chunk 155 optimal weight:    7.9990
   chunk 244 optimal weight:    5.9990
   chunk 183 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 166 GLN
A 234 GLN
B  41 HIS
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 GLN
D  41 HIS
K 220 HIS
** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 249 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.061052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.046943 restraints weight = 197271.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.046222 restraints weight = 100094.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.046472 restraints weight = 79064.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.046692 restraints weight = 59913.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.046777 restraints weight = 55180.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  22924  Z= 0.186
  Angle     :  0.588  11.037  30844  Z= 0.316
  Chirality :  0.036   0.383   3488
  Planarity :  0.004   0.034   4012
  Dihedral  :  3.016  16.744   3074
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.65 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.54 (0.14), residues: 2784
  helix:  3.21 (0.09), residues: 2584
  sheet:  None (None), residues: 0
  loop : -0.70 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 196 
 TYR   0.024   0.002   TYR I 155 
 PHE   0.022   0.002   PHE J 230 
 TRP   0.010   0.001   TRP A  55 
 HIS   0.006   0.001   HIS G  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (22924)
  covalent geometry    : angle       0.58791 (30844)
  hydrogen bonds       : bond        0.06980 ( 2185)
  hydrogen bonds       : angle       4.03265 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.8139 (tmm) cc_final: 0.7883 (tmm)
REVERT: B  235 MET cc_start: 0.8403 (tmm) cc_final: 0.8162 (tmm)
REVERT: C   60 MET cc_start: 0.7687 (tmm) cc_final: 0.7372 (ttm)
REVERT: C  179 LEU cc_start: 0.9258 (tp) cc_final: 0.8811 (pp)
REVERT: C  229 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8348 (t0)
REVERT: G   60 MET cc_start: 0.8826 (tpp) cc_final: 0.8546 (tpp)
REVERT: H  237 TYR cc_start: 0.8256 (t80) cc_final: 0.8044 (t80)
REVERT: J   60 MET cc_start: 0.9540 (mmm) cc_final: 0.9192 (mmm)
REVERT: J  143 PHE cc_start: 0.8981 (t80) cc_final: 0.8750 (t80)
REVERT: J  245 MET cc_start: 0.8840 (tpt) cc_final: 0.8529 (tpp)
REVERT: K  100 TYR cc_start: 0.9189 (m-10) cc_final: 0.8986 (m-10)
  outliers start: 27
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1359
  time to fit residues: 30.4227
Evaluate side-chains
  100 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain C residue  229 ASP
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue   47 SER
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain L residue   83 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 244 optimal weight:    5.9990
   chunk 263 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0040
   chunk 169 optimal weight:    9.9990
   chunk 184 optimal weight:    9.9990
   chunk 150 optimal weight:    9.9990
   chunk 162 optimal weight:    6.9990
   chunk 206 optimal weight:    0.2980
   chunk 50 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 171 optimal weight:    1.9990
   overall best weight:    3.0598

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
B 228 ASN
E 222 HIS
E 251 GLN
F 116 ASN
H 116 ASN
** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 243 GLN
I 249 GLN
J 116 ASN
J 234 GLN
** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.059108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.045241 restraints weight = 201652.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.044293 restraints weight = 111087.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.044486 restraints weight = 91774.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.044741 restraints weight = 67903.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.044783 restraints weight = 63148.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  22924  Z= 0.166
  Angle     :  0.546  12.569  30844  Z= 0.286
  Chirality :  0.034   0.197   3488
  Planarity :  0.004   0.040   4012
  Dihedral  :  3.098  18.286   3068
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.02 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.24 (0.14), residues: 2784
  helix:  3.68 (0.09), residues: 2576
  sheet:  None (None), residues: 0
  loop : -0.55 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 127 
 TYR   0.021   0.002   TYR D 238 
 PHE   0.018   0.002   PHE I 230 
 TRP   0.008   0.001   TRP A  55 
 HIS   0.005   0.001   HIS E  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (22924)
  covalent geometry    : angle       0.54627 (30844)
  hydrogen bonds       : bond        0.05999 ( 2185)
  hydrogen bonds       : angle       3.66231 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 MET cc_start: 0.8498 (ttp) cc_final: 0.8156 (ttt)
REVERT: B  235 MET cc_start: 0.8383 (tmm) cc_final: 0.7935 (tmm)
REVERT: C   60 MET cc_start: 0.7794 (tmm) cc_final: 0.7484 (ttm)
REVERT: D   19 LEU cc_start: 0.9634 (mt) cc_final: 0.9433 (pp)
REVERT: E  245 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7737 (ttm)
REVERT: F  235 MET cc_start: 0.8268 (tpp) cc_final: 0.7675 (tpp)
REVERT: G   60 MET cc_start: 0.8777 (tpp) cc_final: 0.8534 (tpp)
REVERT: H  237 TYR cc_start: 0.8214 (t80) cc_final: 0.7860 (t80)
REVERT: J  235 MET cc_start: 0.9519 (tmm) cc_final: 0.9299 (tmm)
REVERT: J  245 MET cc_start: 0.8889 (tpt) cc_final: 0.8537 (tpp)
REVERT: L  238 TYR cc_start: 0.9554 (m-80) cc_final: 0.9292 (m-80)
  outliers start: 31
  outliers final: 20
  residues processed: 123
  average time/residue: 0.1428
  time to fit residues: 29.0837
Evaluate side-chains
  107 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain C residue  121 CYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain I residue   84 ASP
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue   19 LEU
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue   67 LEU
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue   83 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 264 optimal weight:   10.0000
   chunk 267 optimal weight:    9.9990
   chunk 260 optimal weight:   30.0000
   chunk 143 optimal weight:    2.9990
   chunk 198 optimal weight:    5.9990
   chunk 262 optimal weight:    8.9990
   chunk 142 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 230 optimal weight:   30.0000
   chunk 199 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN
D  41 HIS
D 228 ASN
** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 249 GLN
** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 251 GLN
H 222 HIS
** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 222 HIS
** I 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 251 GLN
J 249 GLN
K 228 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.056211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.040772 restraints weight = 205665.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.040424 restraints weight = 103166.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.040494 restraints weight = 77559.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.040828 restraints weight = 61570.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.040795 restraints weight = 53100.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  22924  Z= 0.276
  Angle     :  0.693  10.346  30844  Z= 0.372
  Chirality :  0.038   0.177   3488
  Planarity :  0.005   0.046   4012
  Dihedral  :  3.558  20.386   3068
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.50 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.08 (0.14), residues: 2784
  helix:  2.92 (0.09), residues: 2568
  sheet:  None (None), residues: 0
  loop : -0.64 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 196 
 TYR   0.030   0.003   TYR A 238 
 PHE   0.028   0.002   PHE I 230 
 TRP   0.012   0.002   TRP C  55 
 HIS   0.007   0.001   HIS D 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (22924)
  covalent geometry    : angle       0.69274 (30844)
  hydrogen bonds       : bond        0.06661 ( 2185)
  hydrogen bonds       : angle       4.17904 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 82
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  235 MET cc_start: 0.8400 (tmm) cc_final: 0.8183 (tmm)
REVERT: C  179 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9060 (mt)
REVERT: E  245 MET cc_start: 0.9097 (ttm) cc_final: 0.7780 (ttt)
REVERT: F  235 MET cc_start: 0.8640 (tpp) cc_final: 0.8299 (tpt)
REVERT: G  235 MET cc_start: 0.9392 (tmm) cc_final: 0.9147 (tpp)
REVERT: G  245 MET cc_start: 0.9348 (ttm) cc_final: 0.9120 (ttm)
REVERT: H  237 TYR cc_start: 0.8559 (t80) cc_final: 0.8260 (t80)
REVERT: J   60 MET cc_start: 0.9586 (mmm) cc_final: 0.9036 (mmm)
REVERT: J  235 MET cc_start: 0.9369 (tmm) cc_final: 0.9137 (tmm)
REVERT: J  245 MET cc_start: 0.8908 (tpt) cc_final: 0.8540 (tpp)
REVERT: K  143 PHE cc_start: 0.9500 (t80) cc_final: 0.9270 (m-80)
REVERT: K  245 MET cc_start: 0.8913 (mtp) cc_final: 0.8655 (ptm)
REVERT: L   60 MET cc_start: 0.9488 (ptt) cc_final: 0.9165 (ppp)
  outliers start: 38
  outliers final: 25
  residues processed: 117
  average time/residue: 0.1440
  time to fit residues: 28.2328
Evaluate side-chains
  100 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain I residue   84 ASP
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue   19 LEU
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue   67 LEU
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue   83 LEU
Chi-restraints excluded: chain L residue  143 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 225 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 233 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 275 optimal weight:   10.0000
   chunk 212 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9980
   chunk 146 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN
C 166 GLN
D  41 HIS
D 228 ASN
K  41 HIS
K 249 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.058012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.044519 restraints weight = 201078.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.043604 restraints weight = 105003.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.043765 restraints weight = 83637.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.043809 restraints weight = 65096.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.043884 restraints weight = 60808.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  22924  Z= 0.127
  Angle     :  0.495  14.145  30844  Z= 0.254
  Chirality :  0.031   0.133   3488
  Planarity :  0.003   0.036   4012
  Dihedral  :  3.134  16.947   3068
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.17 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.50 (0.14), residues: 2784
  helix:  3.84 (0.09), residues: 2572
  sheet:  None (None), residues: 0
  loop : -0.33 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L 178 
 TYR   0.023   0.001   TYR G 155 
 PHE   0.015   0.001   PHE L 230 
 TRP   0.007   0.001   TRP F  55 
 HIS   0.005   0.001   HIS I  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (22924)
  covalent geometry    : angle       0.49452 (30844)
  hydrogen bonds       : bond        0.05395 ( 2185)
  hydrogen bonds       : angle       3.38498 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  232 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: B  235 MET cc_start: 0.8216 (tmm) cc_final: 0.7729 (tmm)
REVERT: C   60 MET cc_start: 0.7966 (ttp) cc_final: 0.6953 (tmm)
REVERT: C  179 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8488 (mt)
REVERT: E  245 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.7610 (ttt)
REVERT: F  235 MET cc_start: 0.8487 (tpp) cc_final: 0.8244 (tpt)
REVERT: H  101 MET cc_start: 0.8907 (mmp) cc_final: 0.8697 (mmt)
REVERT: H  237 TYR cc_start: 0.8155 (t80) cc_final: 0.7731 (t80)
REVERT: I  235 MET cc_start: 0.9107 (tpp) cc_final: 0.8221 (tpp)
REVERT: J   60 MET cc_start: 0.9552 (mmm) cc_final: 0.9025 (mmm)
REVERT: K  143 PHE cc_start: 0.9503 (t80) cc_final: 0.9191 (m-80)
REVERT: K  237 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8501 (t80)
REVERT: K  245 MET cc_start: 0.8859 (mtp) cc_final: 0.8338 (ttp)
REVERT: L   60 MET cc_start: 0.9422 (ptt) cc_final: 0.9181 (ptt)
  outliers start: 31
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1501
  time to fit residues: 26.8587
Evaluate side-chains
  100 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain J residue   19 LEU
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 153 optimal weight:    7.9990
   chunk 176 optimal weight:    6.9990
   chunk 209 optimal weight:   20.0000
   chunk 125 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 215 optimal weight:   10.0000
   chunk 164 optimal weight:    8.9990
   chunk 207 optimal weight:   30.0000
   chunk 56 optimal weight:    0.7980
   chunk 160 optimal weight:    5.9990
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
D  41 HIS
E 228 ASN
** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 243 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.056328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.041084 restraints weight = 205604.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.040876 restraints weight = 117908.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.040930 restraints weight = 83478.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.041077 restraints weight = 66878.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.041113 restraints weight = 56638.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.5862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  22924  Z= 0.218
  Angle     :  0.617  11.604  30844  Z= 0.319
  Chirality :  0.035   0.292   3488
  Planarity :  0.004   0.041   4012
  Dihedral  :  3.288  18.629   3068
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.91 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.89 (0.15), residues: 2784
  helix:  3.44 (0.09), residues: 2572
  sheet:  None (None), residues: 0
  loop : -0.36 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 225 
 TYR   0.023   0.002   TYR G 155 
 PHE   0.016   0.002   PHE D 230 
 TRP   0.009   0.001   TRP C  55 
 HIS   0.014   0.001   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (22924)
  covalent geometry    : angle       0.61691 (30844)
  hydrogen bonds       : bond        0.05787 ( 2185)
  hydrogen bonds       : angle       3.78477 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 76
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  235 MET cc_start: 0.8341 (tmm) cc_final: 0.8054 (tmm)
REVERT: C  179 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8605 (mt)
REVERT: C  235 MET cc_start: 0.7603 (tmm) cc_final: 0.7319 (tmm)
REVERT: D   60 MET cc_start: 0.8130 (ttt) cc_final: 0.7698 (tmm)
REVERT: E  235 MET cc_start: 0.9171 (tpp) cc_final: 0.8797 (tpp)
REVERT: E  245 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.7786 (ttt)
REVERT: F  235 MET cc_start: 0.8604 (tpp) cc_final: 0.8317 (tpt)
REVERT: G  245 MET cc_start: 0.9244 (ttm) cc_final: 0.8936 (ttm)
REVERT: H  237 TYR cc_start: 0.8519 (t80) cc_final: 0.8130 (t80)
REVERT: H  245 MET cc_start: 0.9359 (tpp) cc_final: 0.8957 (ttm)
REVERT: I  230 PHE cc_start: 0.9590 (t80) cc_final: 0.9382 (t80)
REVERT: I  238 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8965 (t80)
REVERT: J   60 MET cc_start: 0.9560 (mmm) cc_final: 0.9029 (mmm)
REVERT: J  245 MET cc_start: 0.8924 (tpt) cc_final: 0.8564 (tpp)
REVERT: K  134 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8632 (tm-30)
REVERT: K  143 PHE cc_start: 0.9518 (t80) cc_final: 0.9245 (m-80)
REVERT: K  245 MET cc_start: 0.8986 (mtp) cc_final: 0.8583 (ttm)
REVERT: L   60 MET cc_start: 0.9401 (ptt) cc_final: 0.9179 (ptt)
REVERT: L  245 MET cc_start: 0.6980 (ptm) cc_final: 0.6291 (ptm)
  outliers start: 38
  outliers final: 26
  residues processed: 109
  average time/residue: 0.1482
  time to fit residues: 27.1710
Evaluate side-chains
  104 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain I residue   84 ASP
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain I residue  238 TYR
Chi-restraints excluded: chain J residue   19 LEU
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   67 LEU
Chi-restraints excluded: chain K residue  134 GLU
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue   83 LEU
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 192 optimal weight:   20.0000
   chunk 228 optimal weight:    9.9990
   chunk 203 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 216 optimal weight:    4.9990
   chunk 196 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 252 optimal weight:    9.9990
   chunk 119 optimal weight:    0.9990
   chunk 178 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** G 222 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 = 0.3757 r_free = 0.3757 target = 0.056358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.039889 restraints weight = 203728.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.040685 restraints weight = 100181.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.040855 restraints weight = 55654.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.040862 restraints weight = 54729.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.040873 restraints weight = 49068.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  22924  Z= 0.192
  Angle     :  0.579  11.786  30844  Z= 0.300
  Chirality :  0.034   0.383   3488
  Planarity :  0.003   0.038   4012
  Dihedral  :  3.284  18.572   3068
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.49 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.85 (0.15), residues: 2784
  helix:  3.41 (0.09), residues: 2572
  sheet:  None (None), residues: 0
  loop : -0.38 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 225 
 TYR   0.018   0.002   TYR G 155 
 PHE   0.049   0.002   PHE I 143 
 TRP   0.006   0.001   TRP C  55 
 HIS   0.005   0.001   HIS G 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (22924)
  covalent geometry    : angle       0.57910 (30844)
  hydrogen bonds       : bond        0.05634 ( 2185)
  hydrogen bonds       : angle       3.71957 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 74
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  235 MET cc_start: 0.8443 (tmm) cc_final: 0.8123 (tmm)
REVERT: C   60 MET cc_start: 0.8159 (ttp) cc_final: 0.7086 (tmm)
REVERT: C  179 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8615 (mt)
REVERT: C  235 MET cc_start: 0.8036 (tmm) cc_final: 0.7736 (tmm)
REVERT: D   60 MET cc_start: 0.8026 (ttt) cc_final: 0.7654 (tmm)
REVERT: F  235 MET cc_start: 0.8725 (tpp) cc_final: 0.8479 (tpt)
REVERT: G  101 MET cc_start: 0.8325 (ptt) cc_final: 0.7812 (ppp)
REVERT: G  134 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (tm-30)
REVERT: H  237 TYR cc_start: 0.8377 (t80) cc_final: 0.7920 (t80)
REVERT: I  235 MET cc_start: 0.8943 (tpp) cc_final: 0.8064 (tpp)
REVERT: I  238 TYR cc_start: 0.9447 (OUTLIER) cc_final: 0.9050 (t80)
REVERT: J   60 MET cc_start: 0.9601 (mmm) cc_final: 0.9052 (mmm)
REVERT: J  114 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8440 (m-80)
REVERT: K  143 PHE cc_start: 0.9628 (t80) cc_final: 0.9349 (m-80)
REVERT: K  245 MET cc_start: 0.8921 (mtp) cc_final: 0.8589 (ttm)
REVERT: L   60 MET cc_start: 0.9428 (ptt) cc_final: 0.9212 (ptm)
REVERT: L  245 MET cc_start: 0.7243 (ptm) cc_final: 0.6536 (ptm)
  outliers start: 40
  outliers final: 32
  residues processed: 109
  average time/residue: 0.1506
  time to fit residues: 27.7888
Evaluate side-chains
  107 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 71
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  134 GLU
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain I residue  238 TYR
Chi-restraints excluded: chain J residue   19 LEU
Chi-restraints excluded: chain J residue  114 TYR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue   67 LEU
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue   83 LEU
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 24 optimal weight:    0.0000
   chunk 133 optimal weight:    4.9990
   chunk 229 optimal weight:   40.0000
   chunk 102 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 88 optimal weight:   40.0000
   chunk 190 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9990
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.057949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.041969 restraints weight = 201557.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.042381 restraints weight = 103608.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042973 restraints weight = 59886.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042900 restraints weight = 44882.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.042911 restraints weight = 45956.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.6354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  22924  Z= 0.119
  Angle     :  0.501  12.536  30844  Z= 0.254
  Chirality :  0.032   0.297   3488
  Planarity :  0.003   0.039   4012
  Dihedral  :  3.102  20.918   3068
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.11 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.75 (0.15), residues: 2784
  helix:  4.02 (0.09), residues: 2568
  sheet:  None (None), residues: 0
  loop : -0.34 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 204 
 TYR   0.033   0.001   TYR L 100 
 PHE   0.055   0.001   PHE L 230 
 TRP   0.008   0.001   TRP F  55 
 HIS   0.005   0.001   HIS G 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (22924)
  covalent geometry    : angle       0.50051 (30844)
  hydrogen bonds       : bond        0.04865 ( 2185)
  hydrogen bonds       : angle       3.25942 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 ASP cc_start: 0.8807 (m-30) cc_final: 0.8581 (t70)
REVERT: B  235 MET cc_start: 0.8262 (tmm) cc_final: 0.7857 (tmm)
REVERT: C   60 MET cc_start: 0.8010 (ttp) cc_final: 0.7082 (tmm)
REVERT: C  235 MET cc_start: 0.7967 (tmm) cc_final: 0.7704 (tmm)
REVERT: D  125 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (tp40)
REVERT: D  245 MET cc_start: 0.8614 (tpp) cc_final: 0.8391 (tpp)
REVERT: G  101 MET cc_start: 0.8222 (ptt) cc_final: 0.7706 (ptt)
REVERT: H  237 TYR cc_start: 0.8332 (t80) cc_final: 0.8117 (t80)
REVERT: I  235 MET cc_start: 0.8963 (tpp) cc_final: 0.8132 (tpp)
REVERT: J   60 MET cc_start: 0.9612 (mmm) cc_final: 0.9088 (mmm)
REVERT: J  101 MET cc_start: 0.9402 (ptt) cc_final: 0.8971 (ppp)
REVERT: J  114 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8365 (m-80)
REVERT: J  121 CYS cc_start: 0.9388 (t) cc_final: 0.9012 (p)
REVERT: K  100 TYR cc_start: 0.9337 (m-10) cc_final: 0.9119 (m-10)
REVERT: K  143 PHE cc_start: 0.9622 (t80) cc_final: 0.9348 (m-80)
REVERT: K  245 MET cc_start: 0.8954 (mtp) cc_final: 0.8643 (ttm)
REVERT: L   60 MET cc_start: 0.9424 (ptt) cc_final: 0.9211 (ptm)
REVERT: L  245 MET cc_start: 0.7521 (ptm) cc_final: 0.6940 (ptm)
  outliers start: 24
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1598
  time to fit residues: 27.4696
Evaluate side-chains
  92 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue  114 TYR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 123 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 120 optimal weight:    0.7980
   chunk 178 optimal weight:    8.9990
   chunk 139 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 220 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
K  41 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.057363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.043931 restraints weight = 202707.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.042819 restraints weight = 105666.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.043190 restraints weight = 86416.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.043167 restraints weight = 68561.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.043233 restraints weight = 65949.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.6497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  22924  Z= 0.128
  Angle     :  0.518  11.231  30844  Z= 0.265
  Chirality :  0.032   0.240   3488
  Planarity :  0.003   0.039   4012
  Dihedral  :  3.097  20.856   3068
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.31 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.70 (0.15), residues: 2784
  helix:  3.96 (0.09), residues: 2580
  sheet:  None (None), residues: 0
  loop : -0.28 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 178 
 TYR   0.024   0.001   TYR J 100 
 PHE   0.022   0.001   PHE L 230 
 TRP   0.007   0.001   TRP K  55 
 HIS   0.005   0.001   HIS G  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (22924)
  covalent geometry    : angle       0.51767 (30844)
  hydrogen bonds       : bond        0.04908 ( 2185)
  hydrogen bonds       : angle       3.33196 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7470 (mm)
REVERT: C   60 MET cc_start: 0.8096 (ttp) cc_final: 0.7092 (tmm)
REVERT: C  179 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8755 (mt)
REVERT: C  235 MET cc_start: 0.8023 (tmm) cc_final: 0.7605 (tmm)
REVERT: D   60 MET cc_start: 0.7974 (ttt) cc_final: 0.7712 (ttt)
REVERT: E  245 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7380 (ttt)
REVERT: F  235 MET cc_start: 0.8527 (tpp) cc_final: 0.7840 (tpp)
REVERT: G  134 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8574 (tm-30)
REVERT: G  235 MET cc_start: 0.8997 (tpp) cc_final: 0.8775 (tpp)
REVERT: I  143 PHE cc_start: 0.9183 (m-10) cc_final: 0.8947 (m-80)
REVERT: I  245 MET cc_start: 0.9302 (ttt) cc_final: 0.8488 (ppp)
REVERT: J   60 MET cc_start: 0.9604 (mmm) cc_final: 0.9079 (mmm)
REVERT: J  114 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8173 (m-80)
REVERT: J  121 CYS cc_start: 0.9379 (t) cc_final: 0.9026 (p)
REVERT: J  245 MET cc_start: 0.8866 (tpt) cc_final: 0.8350 (tpt)
REVERT: K  143 PHE cc_start: 0.9569 (t80) cc_final: 0.9304 (m-80)
REVERT: L   60 MET cc_start: 0.9404 (ptt) cc_final: 0.9184 (ptm)
REVERT: L  245 MET cc_start: 0.7890 (ptm) cc_final: 0.7304 (ptm)
  outliers start: 27
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1475
  time to fit residues: 23.6357
Evaluate side-chains
  94 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  235 MET
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain G residue  134 GLU
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue  114 TYR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 178 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0030
   chunk 14 optimal weight:    8.9990
   chunk 237 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    4.5998

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

Flipped N/Q/H residues before XYZ refinement:
D 228 ASN
** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 228 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.056018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.040067 restraints weight = 204071.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.040275 restraints weight = 105396.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.040427 restraints weight = 66752.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.040479 restraints weight = 56658.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.040516 restraints weight = 51262.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.6729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  22924  Z= 0.211
  Angle     :  0.629  11.601  30844  Z= 0.328
  Chirality :  0.035   0.212   3488
  Planarity :  0.004   0.040   4012
  Dihedral  :  3.373  20.156   3068
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.19 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.91 (0.15), residues: 2784
  helix:  3.43 (0.09), residues: 2584
  sheet:  None (None), residues: 0
  loop : -0.30 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 196 
 TYR   0.048   0.002   TYR J 100 
 PHE   0.045   0.002   PHE L 230 
 TRP   0.008   0.001   TRP C  55 
 HIS   0.010   0.001   HIS K  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (22924)
  covalent geometry    : angle       0.62938 (30844)
  hydrogen bonds       : bond        0.05583 ( 2185)
  hydrogen bonds       : angle       3.76114 ( 6555)

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

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

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5568 Ramachandran restraints generated.
    2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.8344 (tmm) cc_final: 0.8030 (tmm)
REVERT: C  179 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8671 (mt)
REVERT: C  235 MET cc_start: 0.7681 (tmm) cc_final: 0.7384 (tmm)
REVERT: G  245 MET cc_start: 0.9231 (ttm) cc_final: 0.8920 (ttm)
REVERT: I  245 MET cc_start: 0.9480 (ttt) cc_final: 0.8827 (ppp)
REVERT: J   60 MET cc_start: 0.9612 (mmm) cc_final: 0.9090 (mmm)
REVERT: J  101 MET cc_start: 0.9394 (ptt) cc_final: 0.9019 (ppp)
REVERT: J  114 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8374 (m-80)
REVERT: J  121 CYS cc_start: 0.9474 (t) cc_final: 0.9001 (p)
REVERT: J  245 MET cc_start: 0.8961 (tpt) cc_final: 0.8515 (tpt)
REVERT: K  143 PHE cc_start: 0.9646 (t80) cc_final: 0.9382 (m-80)
REVERT: K  245 MET cc_start: 0.8771 (mtp) cc_final: 0.8456 (ptm)
REVERT: L   60 MET cc_start: 0.9444 (ptt) cc_final: 0.9236 (ptm)
REVERT: L  245 MET cc_start: 0.7812 (ptm) cc_final: 0.7165 (ptm)
  outliers start: 28
  outliers final: 19
  residues processed: 97
  average time/residue: 0.1337
  time to fit residues: 21.7805
Evaluate side-chains
  88 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  230 PHE
Chi-restraints excluded: chain E residue  245 MET
Chi-restraints excluded: chain F residue  121 CYS
Chi-restraints excluded: chain I residue  147 LEU
Chi-restraints excluded: chain J residue  114 TYR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain K residue   41 HIS
Chi-restraints excluded: chain K residue  230 PHE
Chi-restraints excluded: chain K residue  237 TYR
Chi-restraints excluded: chain K residue  242 TYR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain L residue  188 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 276
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 113 optimal weight:    7.9990
   chunk 256 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 202 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 215 optimal weight:   20.0000
   chunk 179 optimal weight:    1.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
K  41 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.056609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.041293 restraints weight = 202157.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.040955 restraints weight = 119392.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.041129 restraints weight = 77497.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.041152 restraints weight = 74274.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.041636 restraints weight = 58813.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.6849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  22924  Z= 0.144
  Angle     :  0.559  14.409  30844  Z= 0.286
  Chirality :  0.034   0.231   3488
  Planarity :  0.003   0.040   4012
  Dihedral  :  3.291  20.779   3068
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.52 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.27 (0.15), residues: 2784
  helix:  3.68 (0.09), residues: 2580
  sheet:  None (None), residues: 0
  loop : -0.26 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 196 
 TYR   0.046   0.002   TYR J 100 
 PHE   0.018   0.001   PHE I 230 
 TRP   0.005   0.001   TRP G  55 
 HIS   0.005   0.001   HIS I  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (22924)
  covalent geometry    : angle       0.55914 (30844)
  hydrogen bonds       : bond        0.05203 ( 2185)
  hydrogen bonds       : angle       3.52805 ( 6555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4127.00 seconds
wall clock time: 72 minutes 9.62 seconds (4329.62 seconds total)