Starting phenix.real_space_refine
on Thu Mar 13 04:49:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykw_39374/03_2025/8ykw_39374_neut.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.081
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      55      5.16       5
     C    5574      2.51       5
     N    1481      2.21       5
     O    1608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8718
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1713
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2560
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "E"
      Number of atoms: 1719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1719
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "G"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 440
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2278
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 12, 'TRANS': 271}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SIN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.10, per 1000 atoms: 0.58
  Number of scatterers: 8718
  At special positions: 0
  Unit cell: (86.1, 119.72, 135.3, 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      55     16.00
     O    1608      8.00
     N    1481      7.00
     C    5574      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 268 " distance=2.30

  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      39.2% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.746A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.407A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.161A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.951A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.701A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 11 through 24
    Processing helix  chain 'R' and resid 24 through 49
    Processing helix  chain 'R' and resid 56 through 74
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.008A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
      removed outlier: 3.664A  pdb=" N   ILE R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 131 through 134
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 180 through 196
      removed outlier: 3.603A  pdb=" N   ILE R 186 " --> pdb=" O   ASN R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 217
    Processing helix  chain 'R' and resid 227 through 260
      removed outlier: 3.563A  pdb=" N   VAL R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 3.534A  pdb=" N   ILE R 273 " --> pdb=" O   THR R 269 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL R 279 " --> pdb=" O   SER R 275 " (cutoff:3.500A)
      Proline residue:  R 282  - end of helix
    Processing helix  chain 'R' and resid 286 through 297
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.082A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.664A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.690A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.746A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.257A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.545A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.421A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.725A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.938A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.416A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.375A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.869A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1308 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1410
        1.31 -     1.44: 2459
        1.44 -     1.57: 4948
        1.57 -     1.69: 2
        1.69 -     1.82: 78
  Bond restraints: 8897
  Sorted by residual:
  bond pdb=" CA  LEU E 233 "
       pdb=" C   LEU E 233 "
    ideal  model  delta    sigma   weight residual
    1.524  1.451  0.073 1.32e-02 5.74e+03 3.05e+01
  bond pdb=" CA  LEU E 237 "
       pdb=" C   LEU E 237 "
    ideal  model  delta    sigma   weight residual
    1.523  1.460  0.063 1.30e-02 5.92e+03 2.37e+01
  bond pdb=" CA  VAL A 233 "
       pdb=" C   VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.524  1.473  0.051 1.08e-02 8.57e+03 2.21e+01
  bond pdb=" CA  THR R 246 "
       pdb=" C   THR R 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.571 -0.049 1.17e-02 7.31e+03 1.77e+01
  bond pdb=" C   LEU E 237 "
       pdb=" O   LEU E 237 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.23e-02 6.61e+03 1.53e+01
  ... (remaining 8892 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 11888
        2.25 -     4.50: 145
        4.50 -     6.74: 20
        6.74 -     8.99: 7
        8.99 -    11.24: 1
  Bond angle restraints: 12061
  Sorted by residual:
  angle pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
        pdb=" CA  PRO R 230 "
      ideal   model   delta    sigma   weight residual
     119.05  111.98    7.07 1.11e+00 8.12e-01 4.06e+01
  angle pdb=" N   GLN R 270 "
        pdb=" CA  GLN R 270 "
        pdb=" C   GLN R 270 "
      ideal   model   delta    sigma   weight residual
     112.23  104.57    7.66 1.26e+00 6.30e-01 3.70e+01
  angle pdb=" N   LEU A 232 "
        pdb=" CA  LEU A 232 "
        pdb=" C   LEU A 232 "
      ideal   model   delta    sigma   weight residual
     110.55  102.91    7.64 1.35e+00 5.49e-01 3.20e+01
  angle pdb=" O   LYS R 229 "
        pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
      ideal   model   delta    sigma   weight residual
     120.48  124.76   -4.28 8.90e-01 1.26e+00 2.31e+01
  angle pdb=" CA  LYS R 229 "
        pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
      ideal   model   delta    sigma   weight residual
     120.77  116.60    4.17 9.70e-01 1.06e+00 1.85e+01
  ... (remaining 12056 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4725
       17.91 -    35.82: 410
       35.82 -    53.73: 107
       53.73 -    71.63: 14
       71.63 -    89.54: 8
  Dihedral angle restraints: 5264
    sinusoidal: 1998
      harmonic: 3266
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1182
       0.055 -    0.109: 156
       0.109 -    0.164: 37
       0.164 -    0.219: 1
       0.219 -    0.273: 4
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CA  TYR E 235 "
            pdb=" N   TYR E 235 "
            pdb=" C   TYR E 235 "
            pdb=" CB  TYR E 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  ILE R 278 "
            pdb=" N   ILE R 278 "
            pdb=" C   ILE R 278 "
            pdb=" CB  ILE R 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  THR E 238 "
            pdb=" N   THR E 238 "
            pdb=" C   THR E 238 "
            pdb=" CB  THR E 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1377 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 150 "    0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO E 151 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E 151 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 151 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 245 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   PHE R 245 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PHE R 245 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR R 246 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 291 "   -0.037 5.00e-02 4.00e+02   5.59e-02 4.99e+00
        pdb=" N   PRO R 292 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO R 292 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 292 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1688
        2.77 -     3.30: 8501
        3.30 -     3.84: 14751
        3.84 -     4.37: 18209
        4.37 -     4.90: 31450
  Nonbonded interactions: 74599
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ASN R 274 "
            pdb=" N   TYR R 277 "
     model   vdw
     2.313 3.120
  ... (remaining 74594 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.690
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:10.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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      :  0.004   0.073   8897  Z= 0.252
  Angle     :  0.652  11.238  12061  Z= 0.374
  Chirality :  0.043   0.273   1380
  Planarity :  0.005   0.068   1523
  Dihedral  : 14.747  89.543   3153
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 15.09 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1100
  helix:  1.71 (0.27), residues: 383
  sheet:  0.32 (0.29), residues: 307
  loop :  0.27 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  88 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R  34 
 TYR   0.016   0.001   TYR R  83 
 ARG   0.014   0.001   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: B   46 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7854 (ptm160)
REVERT: B  219 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7352 (mmt-90)
REVERT: E   46 GLU cc_start: 0.8026 (tt0) cc_final: 0.7812 (tt0)
REVERT: R  189 MET cc_start: 0.8267 (mmm) cc_final: 0.8018 (mmm)
  outliers start: 5
  outliers final: 2
  residues processed: 146
  average time/residue: 1.3342
  time to fit residues: 206.5624
Evaluate side-chains
  121 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain E residue  193 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
A 269 ASN
A 331 ASN
A 333 GLN
B  75 GLN
B 259 GLN
E  77 ASN
E 179 GLN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.162346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113134 restraints weight = 9909.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.32
r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8897  Z= 0.213
  Angle     :  0.558   9.306  12061  Z= 0.300
  Chirality :  0.043   0.153   1380
  Planarity :  0.004   0.039   1523
  Dihedral  :  4.602  37.607   1221
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.66 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1100
  helix:  2.31 (0.25), residues: 388
  sheet:  0.43 (0.31), residues: 293
  loop :  0.47 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.014   0.001   PHE A 274 
 TYR   0.022   0.001   TYR R  48 
 ARG   0.007   0.001   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8325 (tpp) cc_final: 0.8123 (ttm)
REVERT: A  298 GLU cc_start: 0.8377 (tt0) cc_final: 0.7931 (tt0)
REVERT: B  214 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7990 (mmp80)
REVERT: B  219 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7408 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8163 (m-30) cc_final: 0.7800 (m-30)
REVERT: E   46 GLU cc_start: 0.8383 (tt0) cc_final: 0.8090 (tt0)
REVERT: E  229 CYS cc_start: 0.8736 (p) cc_final: 0.8508 (p)
REVERT: R  189 MET cc_start: 0.8420 (mmm) cc_final: 0.8019 (mmm)
REVERT: R  193 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (tt)
REVERT: R  253 ASN cc_start: 0.8774 (m-40) cc_final: 0.8447 (m-40)
  outliers start: 24
  outliers final: 9
  residues processed: 151
  average time/residue: 1.2790
  time to fit residues: 205.1791
Evaluate side-chains
  129 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 79 optimal weight:    0.3980
   chunk 73 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
A 331 ASN
B  75 GLN
B 259 GLN
E  39 GLN
E  77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.161971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113060 restraints weight = 10108.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.30
r_work: 0.3216 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8897  Z= 0.201
  Angle     :  0.529   9.485  12061  Z= 0.283
  Chirality :  0.042   0.142   1380
  Planarity :  0.004   0.038   1523
  Dihedral  :  4.228  24.454   1218
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.27 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1100
  helix:  2.59 (0.25), residues: 388
  sheet:  0.51 (0.30), residues: 291
  loop :  0.37 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.011   0.001   PHE R 115 
 TYR   0.023   0.001   TYR R  48 
 ARG   0.005   0.000   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8206 (mpt90) cc_final: 0.7972 (mpt90)
REVERT: A  243 MET cc_start: 0.8373 (tpp) cc_final: 0.7992 (ttm)
REVERT: A  255 ASN cc_start: 0.8913 (m-40) cc_final: 0.8711 (m110)
REVERT: A  298 GLU cc_start: 0.8410 (tt0) cc_final: 0.7979 (tt0)
REVERT: B  219 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7505 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8193 (m-30) cc_final: 0.7805 (m-30)
REVERT: E   38 ARG cc_start: 0.8839 (ptt180) cc_final: 0.8632 (ptt-90)
REVERT: E   46 GLU cc_start: 0.8422 (tt0) cc_final: 0.8139 (tt0)
REVERT: E  183 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8143 (mt0)
REVERT: E  202 ARG cc_start: 0.7684 (ptt-90) cc_final: 0.7471 (ptt-90)
REVERT: E  229 CYS cc_start: 0.8778 (p) cc_final: 0.8564 (p)
REVERT: R  189 MET cc_start: 0.8506 (mmm) cc_final: 0.8086 (mmm)
REVERT: R  253 ASN cc_start: 0.8745 (m-40) cc_final: 0.8429 (m-40)
  outliers start: 26
  outliers final: 13
  residues processed: 145
  average time/residue: 1.1961
  time to fit residues: 184.8851
Evaluate side-chains
  136 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  234 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
A 331 ASN
B  75 GLN
E  39 GLN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.159749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109998 restraints weight = 10080.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.33
r_work: 0.3173 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8897  Z= 0.308
  Angle     :  0.575   8.870  12061  Z= 0.303
  Chirality :  0.044   0.156   1380
  Planarity :  0.004   0.050   1523
  Dihedral  :  4.317  20.723   1218
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.06 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.25), residues: 1100
  helix:  2.51 (0.25), residues: 388
  sheet:  0.48 (0.30), residues: 293
  loop :  0.28 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS G  44 
 PHE   0.014   0.002   PHE R 115 
 TYR   0.021   0.001   TYR R  48 
 ARG   0.006   0.001   ARG B 314 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8385 (tpp) cc_final: 0.8170 (ttm)
REVERT: A  297 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8033 (tt0)
REVERT: A  298 GLU cc_start: 0.8381 (tt0) cc_final: 0.7964 (tt0)
REVERT: B  175 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7558 (pp30)
REVERT: B  219 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7272 (mmt180)
REVERT: E   46 GLU cc_start: 0.8455 (tt0) cc_final: 0.8179 (tt0)
REVERT: E  183 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8167 (mt0)
REVERT: E  202 ARG cc_start: 0.7610 (ptt-90) cc_final: 0.7343 (ptt-90)
REVERT: R  253 ASN cc_start: 0.8769 (m-40) cc_final: 0.8517 (m-40)
  outliers start: 34
  outliers final: 17
  residues processed: 151
  average time/residue: 1.1985
  time to fit residues: 193.5402
Evaluate side-chains
  143 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  234 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
B 266 HIS
E  77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.158299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.108491 restraints weight = 10063.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.33
r_work: 0.3154 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8897  Z= 0.367
  Angle     :  0.591   9.417  12061  Z= 0.313
  Chirality :  0.045   0.158   1380
  Planarity :  0.004   0.050   1523
  Dihedral  :  4.474  21.152   1218
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.67 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1100
  helix:  2.32 (0.25), residues: 388
  sheet:  0.40 (0.30), residues: 285
  loop :  0.13 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.008   0.002   HIS B 266 
 PHE   0.018   0.002   PHE A 274 
 TYR   0.022   0.002   TYR R  48 
 ARG   0.005   0.001   ARG B 314 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A  297 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8024 (tt0)
REVERT: B  219 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7243 (mmt180)
REVERT: E   46 GLU cc_start: 0.8410 (tt0) cc_final: 0.8170 (tt0)
REVERT: E  160 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7631 (tpp-160)
REVERT: E  183 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8204 (mt0)
REVERT: R  253 ASN cc_start: 0.8852 (m-40) cc_final: 0.8565 (m-40)
  outliers start: 30
  outliers final: 19
  residues processed: 144
  average time/residue: 1.1158
  time to fit residues: 172.2917
Evaluate side-chains
  144 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  234 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0020
   chunk 84 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
B 237 ASN
B 239 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.160815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110641 restraints weight = 10035.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.39
r_work: 0.3158 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8897  Z= 0.177
  Angle     :  0.533   9.873  12061  Z= 0.280
  Chirality :  0.042   0.165   1380
  Planarity :  0.004   0.046   1523
  Dihedral  :  4.128  21.994   1218
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.53 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1100
  helix:  2.62 (0.25), residues: 388
  sheet:  0.41 (0.30), residues: 283
  loop :  0.14 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS G  44 
 PHE   0.020   0.001   PHE A 274 
 TYR   0.025   0.001   TYR R  48 
 ARG   0.006   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8394 (tt0) cc_final: 0.7981 (tt0)
REVERT: B  175 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7529 (pp30)
REVERT: B  219 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7302 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8284 (m-30) cc_final: 0.8021 (m-30)
REVERT: E   46 GLU cc_start: 0.8378 (tt0) cc_final: 0.8175 (tt0)
REVERT: E  160 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7536 (mmm-85)
REVERT: E  229 CYS cc_start: 0.8746 (p) cc_final: 0.8540 (p)
REVERT: R  253 ASN cc_start: 0.8817 (m-40) cc_final: 0.8566 (m-40)
  outliers start: 24
  outliers final: 13
  residues processed: 149
  average time/residue: 1.2403
  time to fit residues: 198.1562
Evaluate side-chains
  143 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  149 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
E  77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.161596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.112527 restraints weight = 10050.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.34
r_work: 0.3213 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8897  Z= 0.201
  Angle     :  0.536   8.140  12061  Z= 0.282
  Chirality :  0.042   0.171   1380
  Planarity :  0.004   0.041   1523
  Dihedral  :  4.094  22.386   1218
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.61 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1100
  helix:  2.62 (0.26), residues: 389
  sheet:  0.36 (0.30), residues: 285
  loop :  0.21 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.013   0.001   PHE R  34 
 TYR   0.027   0.001   TYR R  48 
 ARG   0.004   0.000   ARG R 217 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8398 (tt0) cc_final: 0.8040 (tt0)
REVERT: B  153 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7768 (p0)
REVERT: B  175 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7596 (pp30)
REVERT: B  219 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7336 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8261 (m-30) cc_final: 0.8005 (m-30)
REVERT: E  160 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7669 (tpp-160)
REVERT: R   64 ASN cc_start: 0.7946 (m110) cc_final: 0.7555 (m-40)
REVERT: R  253 ASN cc_start: 0.8827 (m-40) cc_final: 0.8568 (m-40)
  outliers start: 22
  outliers final: 13
  residues processed: 146
  average time/residue: 1.2833
  time to fit residues: 200.0402
Evaluate side-chains
  141 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 95 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0050
   chunk 99 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
B  75 GLN
R 134 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.163192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.114470 restraints weight = 10075.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.32
r_work: 0.3242 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063   8897  Z= 0.168
  Angle     :  0.531   8.785  12061  Z= 0.276
  Chirality :  0.042   0.167   1380
  Planarity :  0.004   0.041   1523
  Dihedral  :  4.019  22.668   1218
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.91 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1100
  helix:  2.70 (0.26), residues: 389
  sheet:  0.40 (0.31), residues: 283
  loop :  0.20 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.001   HIS G  44 
 PHE   0.009   0.001   PHE R 115 
 TYR   0.031   0.001   TYR R  48 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8362 (tt0) cc_final: 0.8001 (tt0)
REVERT: B  153 ASP cc_start: 0.8237 (m-30) cc_final: 0.7848 (p0)
REVERT: B  175 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7570 (pp30)
REVERT: B  219 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7270 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8190 (m-30) cc_final: 0.7938 (m-30)
REVERT: E   82 GLN cc_start: 0.8171 (tp40) cc_final: 0.7970 (tp-100)
REVERT: E  160 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7649 (tpp-160)
REVERT: R   64 ASN cc_start: 0.7905 (m110) cc_final: 0.7517 (m-40)
REVERT: R  253 ASN cc_start: 0.8829 (m-40) cc_final: 0.8583 (m-40)
  outliers start: 17
  outliers final: 15
  residues processed: 144
  average time/residue: 1.1854
  time to fit residues: 182.2292
Evaluate side-chains
  141 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 94 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 109 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
B 259 GLN
E  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.161951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.112815 restraints weight = 10017.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.31
r_work: 0.3217 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8897  Z= 0.217
  Angle     :  0.544   8.247  12061  Z= 0.287
  Chirality :  0.042   0.205   1380
  Planarity :  0.004   0.039   1523
  Dihedral  :  4.076  22.677   1218
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.01 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.26), residues: 1100
  helix:  2.73 (0.25), residues: 387
  sheet:  0.39 (0.31), residues: 285
  loop :  0.21 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.012   0.001   PHE A 196 
 TYR   0.029   0.001   TYR R  48 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.066 
Fit side-chains
REVERT: A  297 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8043 (tt0)
REVERT: A  298 GLU cc_start: 0.8407 (tt0) cc_final: 0.8116 (tt0)
REVERT: B  153 ASP cc_start: 0.8289 (m-30) cc_final: 0.7938 (p0)
REVERT: B  175 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7655 (pp30)
REVERT: B  219 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7379 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8220 (m-30) cc_final: 0.7974 (m-30)
REVERT: E  160 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7670 (tpp-160)
REVERT: R  193 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7844 (tt)
REVERT: R  253 ASN cc_start: 0.8833 (m-40) cc_final: 0.8575 (m-40)
  outliers start: 17
  outliers final: 15
  residues processed: 139
  average time/residue: 1.2357
  time to fit residues: 183.3745
Evaluate side-chains
  142 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 75 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0270
   chunk 89 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.164014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.115578 restraints weight = 10034.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.30
r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.076   8897  Z= 0.168
  Angle     :  0.530   8.964  12061  Z= 0.277
  Chirality :  0.041   0.179   1380
  Planarity :  0.003   0.041   1523
  Dihedral  :  3.966  22.696   1218
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.34 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.26), residues: 1100
  helix:  2.79 (0.26), residues: 388
  sheet:  0.43 (0.31), residues: 282
  loop :  0.23 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.014   0.001   PHE R  34 
 TYR   0.032   0.001   TYR R  48 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 1.028 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8410 (tt0) cc_final: 0.8069 (tt0)
REVERT: B  175 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7714 (pp30)
REVERT: B  219 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7337 (mmt-90)
REVERT: B  267 ASP cc_start: 0.8217 (m-30) cc_final: 0.7938 (m-30)
REVERT: E  160 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7515 (tpp-160)
REVERT: R  253 ASN cc_start: 0.8801 (m-40) cc_final: 0.8549 (m-40)
  outliers start: 17
  outliers final: 14
  residues processed: 135
  average time/residue: 1.1836
  time to fit residues: 171.0310
Evaluate side-chains
  140 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0670
   chunk 94 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0980
   chunk 52 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.163415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.114675 restraints weight = 10043.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.32
r_work: 0.3244 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8897  Z= 0.182
  Angle     :  0.535   8.435  12061  Z= 0.279
  Chirality :  0.041   0.179   1380
  Planarity :  0.003   0.040   1523
  Dihedral  :  3.958  22.643   1218
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 21.44 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1100
  helix:  2.79 (0.25), residues: 388
  sheet:  0.41 (0.31), residues: 284
  loop :  0.28 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.014   0.001   PHE R  34 
 TYR   0.029   0.001   TYR R  48 
 ARG   0.007   0.000   ARG R 255 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7737.02 seconds
wall clock time: 133 minutes 45.61 seconds (8025.61 seconds total)