Starting phenix.real_space_refine
on Fri Mar 14 00:34:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rkn_24501/03_2025/7rkn_24501.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.004
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      71      5.16       5
     C    5993      2.51       5
     N    1586      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9393
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1736
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2575
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          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: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 404
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1761
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "L"
      Number of atoms: 520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 520
          Classifications: {'peptide': 68}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'PCA:plan-2': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 2397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2397
          Classifications: {'peptide': 294}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 283}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.66, per 1000 atoms: 0.71
  Number of scatterers: 9393
  At special positions: 0
  Unit cell: (99.22, 122.18, 128.74, 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      71     16.00
     O    1743      8.00
     N    1586      7.00
     C    5993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L   8 " - pdb=" SG  CYS L  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  12 " - pdb=" SG  CYS L  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  23 " - pdb=" SG  CYS R 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 104 " - pdb=" SG  CYS R 173 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2262

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      36.4% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.563A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.086A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.512A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 3.672A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.776A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.782A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 352
      removed outlier: 4.367A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 4.148A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 4.059A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.633A  pdb=" N   PHE D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 56
      removed outlier: 3.746A  pdb=" N   SER D  55 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 56'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.054A  pdb=" N   THR D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 56 through 68
      removed outlier: 3.661A  pdb=" N   ASP L  60 " --> pdb=" O   GLN L  56 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN L  63 " --> pdb=" O   LYS L  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 25 through 60
      Proline residue:  R  34  - end of helix
      removed outlier: 4.742A  pdb=" N   LEU R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 93
      removed outlier: 3.608A  pdb=" N   LEU R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
      Proline residue:  R  87  - end of helix
    Processing helix  chain 'R' and resid 103 through 135
      removed outlier: 3.618A  pdb=" N   ILE R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 164
      Proline residue:  R 161  - end of helix
      removed outlier: 3.639A  pdb=" N   MET R 164 " --> pdb=" O   ILE R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 195
    Processing helix  chain 'R' and resid 197 through 216
    Processing helix  chain 'R' and resid 223 through 240
      removed outlier: 3.797A  pdb=" N   VAL R 227 " --> pdb=" O   LYS R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 257
    Processing helix  chain 'R' and resid 262 through 292
      removed outlier: 3.979A  pdb=" N   CYS R 284 " --> pdb=" O   ALA R 280 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   CYS R 285 " --> pdb=" O   PHE R 281 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU R 286 " --> pdb=" O   CYS R 282 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.795A  pdb=" N   TYR R 291 " --> pdb=" O   ASN R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 306
      removed outlier: 3.802A  pdb=" N   GLU R 301 " --> pdb=" O   LYS R 297 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 4.041A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226
      removed outlier: 6.933A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.698A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.207A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.755A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 6.399A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.228A  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: 3.717A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.841A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 317
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.677A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 23
    Processing sheet with id=AB3, first strand: chain 'D' and resid 143 through 148
    Processing sheet with id=AB4, first strand: chain 'D' and resid 174 through 178
      removed outlier: 6.732A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU D 162 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 26 through 29
      removed outlier: 3.951A  pdb=" N   HIS L  26 " --> pdb=" O   GLU L  42 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 167 through 168

    397 hydrogen bonds defined for protein.
    1134 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: 3.08

  Time building geometry restraints manager: 3.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2996
        1.34 -     1.46: 2237
        1.46 -     1.58: 4265
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 9596
  Sorted by residual:
  bond pdb=" N   PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.463 -0.118 2.00e-02 2.50e+03 3.49e+01
  bond pdb=" C   ILE R 160 "
       pdb=" N   PRO R 161 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.53e+00
  bond pdb=" N   GLU R 308 "
       pdb=" CA  GLU R 308 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.10e+00
  bond pdb=" C   ILE R 199 "
       pdb=" N   PRO R 200 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.018 1.30e-02 5.92e+03 2.00e+00
  bond pdb=" CA  THR B  87 "
       pdb=" C   THR B  87 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 1.51e-02 4.39e+03 1.93e+00
  ... (remaining 9591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12688
        2.75 -     5.49: 271
        5.49 -     8.24: 39
        8.24 -    10.98: 9
       10.98 -    13.73: 2
  Bond angle restraints: 13009
  Sorted by residual:
  angle pdb=" CA  CYS B 121 "
        pdb=" CB  CYS B 121 "
        pdb=" SG  CYS B 121 "
      ideal   model   delta    sigma   weight residual
     114.40  128.13  -13.73 2.30e+00 1.89e-01 3.56e+01
  angle pdb=" C   ARG D 179 "
        pdb=" N   MET D 180 "
        pdb=" CA  MET D 180 "
      ideal   model   delta    sigma   weight residual
     121.54  130.11   -8.57 1.91e+00 2.74e-01 2.01e+01
  angle pdb=" C   ALA R 307 "
        pdb=" N   GLU R 308 "
        pdb=" CA  GLU R 308 "
      ideal   model   delta    sigma   weight residual
     121.70  129.70   -8.00 1.80e+00 3.09e-01 1.98e+01
  angle pdb=" C   GLN L  63 "
        pdb=" N   HIS L  64 "
        pdb=" CA  HIS L  64 "
      ideal   model   delta    sigma   weight residual
     121.58  113.88    7.70 1.95e+00 2.63e-01 1.56e+01
  angle pdb=" CB  MET R 174 "
        pdb=" CG  MET R 174 "
        pdb=" SD  MET R 174 "
      ideal   model   delta    sigma   weight residual
     112.70  123.88  -11.18 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 13004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 5256
       17.61 -    35.22: 353
       35.22 -    52.84: 67
       52.84 -    70.45: 13
       70.45 -    88.06: 7
  Dihedral angle restraints: 5696
    sinusoidal: 2195
      harmonic: 3501
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.83   47.83     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CA  TYR A 296 "
           pdb=" C   TYR A 296 "
           pdb=" N   GLU A 297 "
           pdb=" CA  GLU A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CB  CYS R 104 "
           pdb=" SG  CYS R 104 "
           pdb=" SG  CYS R 173 "
           pdb=" CB  CYS R 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -52.96  -33.04     1      1.00e+01 1.00e-02 1.55e+01
  ... (remaining 5693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1304
       0.086 -    0.171: 164
       0.171 -    0.257: 10
       0.257 -    0.342: 1
       0.342 -    0.428: 1
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CB  ILE A 222 "
            pdb=" CA  ILE A 222 "
            pdb=" CG1 ILE A 222 "
            pdb=" CG2 ILE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  LYS R  33 "
            pdb=" N   LYS R  33 "
            pdb=" C   LYS R  33 "
            pdb=" CB  LYS R  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 1641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "   -0.038 2.00e-02 2.50e+03   4.38e-02 4.80e+01
        pdb=" CG  TRP B  82 "    0.110 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "   -0.068 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "   -0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  52 "    0.029 2.00e-02 2.50e+03   5.77e-02 3.33e+01
        pdb=" C   PHE R  52 "   -0.100 2.00e-02 2.50e+03
        pdb=" O   PHE R  52 "    0.037 2.00e-02 2.50e+03
        pdb=" N   LEU R  53 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 320 "    0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   TYR A 320 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   TYR A 320 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 321 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1638 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 823
        2.75 -     3.28: 9651
        3.28 -     3.82: 15379
        3.82 -     4.36: 18595
        4.36 -     4.90: 31856
  Nonbonded interactions: 76304
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   LYS A  35 "
            pdb=" OG1 THR A 219 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   GLY D  33 "
            pdb=" OG  SER D  99 "
     model   vdw
     2.283 3.040
  ... (remaining 76299 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 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:             2.420
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.260
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
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   0.118   9596  Z= 0.293
  Angle     :  0.974  13.731  13009  Z= 0.521
  Chirality :  0.058   0.428   1480
  Planarity :  0.007   0.086   1641
  Dihedral  : 12.675  88.061   3413
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.24), residues: 1182
  helix: -0.08 (0.26), residues: 377
  sheet: -2.46 (0.31), residues: 249
  loop : -1.85 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.110   0.003   TRP B  82 
 HIS   0.014   0.001   HIS L  64 
 PHE   0.058   0.003   PHE R  52 
 TYR   0.016   0.002   TYR D 178 
 ARG   0.010   0.001   ARG B 137 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.035 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2109
  time to fit residues: 46.0141
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 106 optimal weight:    0.1980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
L  46 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.095279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.076285 restraints weight = 23954.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.078401 restraints weight = 12230.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.079844 restraints weight = 7991.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9596  Z= 0.180
  Angle     :  0.591  10.258  13009  Z= 0.312
  Chirality :  0.042   0.140   1480
  Planarity :  0.004   0.056   1641
  Dihedral  :  4.722  41.896   1300
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.74 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.24), residues: 1182
  helix:  0.46 (0.26), residues: 393
  sheet: -2.16 (0.31), residues: 256
  loop : -1.88 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B  82 
 HIS   0.015   0.001   HIS L  64 
 PHE   0.025   0.001   PHE A 334 
 TYR   0.014   0.001   TYR A 320 
 ARG   0.007   0.000   ARG L  47 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7779 (mmp) cc_final: 0.7567 (mmp)
REVERT: B  289 TYR cc_start: 0.8630 (m-80) cc_final: 0.8273 (m-80)
REVERT: D  207 LEU cc_start: 0.8618 (tp) cc_final: 0.8359 (tt)
REVERT: D  218 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7514 (ttt)
REVERT: R   27 ASP cc_start: 0.7197 (p0) cc_final: 0.6934 (p0)
REVERT: R  302 LEU cc_start: 0.8126 (mm) cc_final: 0.7776 (pp)
  outliers start: 13
  outliers final: 7
  residues processed: 139
  average time/residue: 0.2108
  time to fit residues: 42.1122
Evaluate side-chains
  124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 97 optimal weight:    0.4980
   chunk 114 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.094933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.076878 restraints weight = 24404.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.078823 restraints weight = 13923.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.079405 restraints weight = 9262.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9596  Z= 0.165
  Angle     :  0.559   9.987  13009  Z= 0.293
  Chirality :  0.041   0.140   1480
  Planarity :  0.004   0.043   1641
  Dihedral  :  4.519  41.886   1300
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.71 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.45 (0.25), residues: 1182
  helix:  0.78 (0.27), residues: 387
  sheet: -1.88 (0.32), residues: 246
  loop : -1.77 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R  89 
 HIS   0.016   0.001   HIS L  64 
 PHE   0.020   0.001   PHE A 334 
 TYR   0.014   0.001   TYR D 178 
 ARG   0.011   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.068 
Fit side-chains
REVERT: B  289 TYR cc_start: 0.8588 (m-80) cc_final: 0.8268 (m-80)
REVERT: D   46 GLU cc_start: 0.6982 (tt0) cc_final: 0.6773 (tt0)
REVERT: D   76 LYS cc_start: 0.7828 (mttt) cc_final: 0.7441 (tptp)
REVERT: D  218 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7435 (ttt)
REVERT: R   56 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6207 (t80)
  outliers start: 21
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1990
  time to fit residues: 39.3194
Evaluate side-chains
  126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  282 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 106 optimal weight:    0.0170
   chunk 109 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN
R 300 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.094307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.075733 restraints weight = 24007.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.078088 restraints weight = 12777.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.078734 restraints weight = 8046.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9596  Z= 0.159
  Angle     :  0.550   9.874  13009  Z= 0.286
  Chirality :  0.041   0.144   1480
  Planarity :  0.004   0.040   1641
  Dihedral  :  4.364  40.896   1300
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.28 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.28 (0.25), residues: 1182
  helix:  0.86 (0.27), residues: 394
  sheet: -1.67 (0.33), residues: 248
  loop : -1.72 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R  89 
 HIS   0.014   0.001   HIS L  64 
 PHE   0.018   0.001   PHE A 334 
 TYR   0.017   0.001   TYR D 103 
 ARG   0.005   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 TYR cc_start: 0.8820 (t80) cc_final: 0.8571 (t80)
REVERT: B  234 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8903 (m-80)
REVERT: B  275 SER cc_start: 0.9095 (p) cc_final: 0.8725 (m)
REVERT: B  289 TYR cc_start: 0.8686 (m-80) cc_final: 0.8317 (m-80)
REVERT: L   48 LEU cc_start: 0.9006 (mm) cc_final: 0.8595 (tp)
REVERT: R   56 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6283 (t80)
REVERT: R  300 GLN cc_start: 0.7879 (mp-120) cc_final: 0.7660 (mp10)
  outliers start: 20
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1940
  time to fit residues: 39.6351
Evaluate side-chains
  130 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 88 optimal weight:   20.0000
   chunk 75 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.090456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.072013 restraints weight = 23979.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.073428 restraints weight = 13077.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.074975 restraints weight = 8669.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9596  Z= 0.341
  Angle     :  0.618  11.206  13009  Z= 0.324
  Chirality :  0.044   0.175   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.709  42.358   1300
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.44 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.47 (0.25), residues: 1182
  helix:  0.68 (0.26), residues: 394
  sheet: -1.83 (0.31), residues: 271
  loop : -1.75 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R  89 
 HIS   0.014   0.002   HIS L  64 
 PHE   0.015   0.002   PHE D  27 
 TYR   0.015   0.002   TYR D 178 
 ARG   0.008   0.001   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 TYR cc_start: 0.8493 (m-10) cc_final: 0.8272 (m-80)
REVERT: A  324 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8052 (p)
REVERT: B   59 TYR cc_start: 0.8130 (m-80) cc_final: 0.7814 (m-80)
REVERT: B  234 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9099 (m-80)
REVERT: D   76 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7319 (tptp)
REVERT: L   56 GLN cc_start: 0.7877 (mp10) cc_final: 0.7284 (pm20)
REVERT: L   60 ASP cc_start: 0.8320 (t0) cc_final: 0.8060 (t0)
REVERT: R   56 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6456 (t80)
REVERT: R  300 GLN cc_start: 0.7755 (mp-120) cc_final: 0.7443 (mp10)
  outliers start: 26
  outliers final: 15
  residues processed: 136
  average time/residue: 0.1936
  time to fit residues: 38.9669
Evaluate side-chains
  128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue   76 LYS
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 72 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 88 optimal weight:   20.0000
   overall best weight:    0.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.073985 restraints weight = 23776.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075819 restraints weight = 12245.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.076413 restraints weight = 8489.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9596  Z= 0.179
  Angle     :  0.565  10.070  13009  Z= 0.293
  Chirality :  0.042   0.159   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.504  42.858   1300
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.62 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.28 (0.25), residues: 1182
  helix:  0.88 (0.26), residues: 393
  sheet: -1.79 (0.31), residues: 265
  loop : -1.64 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP B  82 
 HIS   0.012   0.001   HIS L  64 
 PHE   0.016   0.001   PHE A 334 
 TYR   0.021   0.001   TYR D 103 
 ARG   0.005   0.000   ARG B  52 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 TYR cc_start: 0.8480 (m-10) cc_final: 0.8228 (m-80)
REVERT: A  324 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7779 (p)
REVERT: D  219 GLN cc_start: 0.8095 (pp30) cc_final: 0.7886 (pp30)
REVERT: L   48 LEU cc_start: 0.8946 (mm) cc_final: 0.8580 (tp)
REVERT: L   56 GLN cc_start: 0.7979 (mp10) cc_final: 0.7419 (pm20)
REVERT: L   66 ASP cc_start: 0.8325 (m-30) cc_final: 0.7930 (p0)
REVERT: R   56 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6417 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1957
  time to fit residues: 38.6685
Evaluate side-chains
  129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.090818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072080 restraints weight = 24180.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.074103 restraints weight = 12639.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.075484 restraints weight = 8309.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9596  Z= 0.208
  Angle     :  0.578  10.181  13009  Z= 0.299
  Chirality :  0.043   0.257   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.497  43.608   1300
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.82 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.32 (0.25), residues: 1182
  helix:  0.87 (0.26), residues: 393
  sheet: -1.88 (0.30), residues: 284
  loop : -1.60 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B  82 
 HIS   0.013   0.001   HIS L  64 
 PHE   0.017   0.001   PHE R 111 
 TYR   0.020   0.001   TYR D 103 
 ARG   0.007   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 TYR cc_start: 0.8448 (m-10) cc_final: 0.8234 (m-80)
REVERT: A  324 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (p)
REVERT: D   34 MET cc_start: 0.7697 (mmm) cc_final: 0.7063 (mtm)
REVERT: D  103 TYR cc_start: 0.7706 (t80) cc_final: 0.7416 (t80)
REVERT: L   48 LEU cc_start: 0.8982 (mm) cc_final: 0.8592 (tp)
REVERT: L   56 GLN cc_start: 0.8035 (mp10) cc_final: 0.7396 (pm20)
REVERT: R   56 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6406 (t80)
REVERT: R  158 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7420 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1842
  time to fit residues: 36.5631
Evaluate side-chains
  127 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 103 optimal weight:   40.0000
   chunk 30 optimal weight:    0.0000
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 73 optimal weight:    9.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.1190

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
R 300 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.090678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072935 restraints weight = 24512.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.074732 restraints weight = 12414.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.075686 restraints weight = 7916.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9596  Z= 0.202
  Angle     :  0.578  10.095  13009  Z= 0.299
  Chirality :  0.043   0.231   1480
  Planarity :  0.004   0.050   1641
  Dihedral  :  4.478  43.709   1300
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.32 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.24 (0.25), residues: 1182
  helix:  0.96 (0.27), residues: 390
  sheet: -1.77 (0.31), residues: 276
  loop : -1.63 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.013   0.001   HIS L  64 
 PHE   0.017   0.001   PHE R 111 
 TYR   0.017   0.001   TYR D 103 
 ARG   0.005   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8097 (tt)
REVERT: A  256 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8471 (m110)
REVERT: A  320 TYR cc_start: 0.8466 (m-10) cc_final: 0.8261 (m-80)
REVERT: A  324 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7761 (p)
REVERT: D   34 MET cc_start: 0.7701 (mmm) cc_final: 0.7093 (mtm)
REVERT: D   76 LYS cc_start: 0.7625 (pttt) cc_final: 0.7045 (tptp)
REVERT: D  103 TYR cc_start: 0.7812 (t80) cc_final: 0.7517 (t80)
REVERT: L   56 GLN cc_start: 0.7992 (mp10) cc_final: 0.7398 (pm20)
REVERT: R   56 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6424 (t80)
REVERT: R  136 MET cc_start: 0.7400 (mmt) cc_final: 0.7171 (mmt)
REVERT: R  158 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7394 (tt)
REVERT: R  168 LYS cc_start: 0.7436 (tptp) cc_final: 0.6536 (tptt)
  outliers start: 25
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1833
  time to fit residues: 37.7996
Evaluate side-chains
  134 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   64 HIS
Chi-restraints excluded: chain R residue   56 PHE
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 112 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 108 optimal weight:    0.0060
   chunk 109 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.9602

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.090034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.071337 restraints weight = 24069.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.073788 restraints weight = 12386.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.074321 restraints weight = 7759.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9596  Z= 0.294
  Angle     :  0.630  10.732  13009  Z= 0.326
  Chirality :  0.044   0.228   1480
  Planarity :  0.004   0.051   1641
  Dihedral  :  4.680  42.638   1300
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.52 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.38 (0.25), residues: 1182
  helix:  0.77 (0.26), residues: 390
  sheet: -1.86 (0.30), residues: 279
  loop : -1.63 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP B  82 
 HIS   0.014   0.001   HIS L  64 
 PHE   0.013   0.001   PHE R 111 
 TYR   0.016   0.002   TYR D 178 
 ARG   0.007   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8185 (tt)
REVERT: A  256 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8272 (m110)
REVERT: A  320 TYR cc_start: 0.8475 (m-10) cc_final: 0.8262 (m-80)
REVERT: A  324 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7994 (p)
REVERT: B   59 TYR cc_start: 0.8055 (m-80) cc_final: 0.7701 (m-80)
REVERT: B   82 TRP cc_start: 0.6547 (m100) cc_final: 0.6330 (m100)
REVERT: D   34 MET cc_start: 0.7717 (mmm) cc_final: 0.7177 (mtm)
REVERT: D   76 LYS cc_start: 0.7859 (pttt) cc_final: 0.7224 (tptp)
REVERT: D  180 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7795 (ptm)
REVERT: D  219 GLN cc_start: 0.8198 (pp30) cc_final: 0.7956 (pp30)
REVERT: L   56 GLN cc_start: 0.7999 (mp10) cc_final: 0.7421 (pm20)
REVERT: L   60 ASP cc_start: 0.8097 (t0) cc_final: 0.7509 (t0)
REVERT: R  158 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7422 (tt)
  outliers start: 27
  outliers final: 17
  residues processed: 140
  average time/residue: 0.1852
  time to fit residues: 37.9561
Evaluate side-chains
  135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0270
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** L  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.090909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.073062 restraints weight = 24259.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.074829 restraints weight = 11965.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.076365 restraints weight = 7666.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9596  Z= 0.179
  Angle     :  0.599  10.242  13009  Z= 0.308
  Chirality :  0.043   0.222   1480
  Planarity :  0.004   0.047   1641
  Dihedral  :  4.577  43.156   1300
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.50 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.27 (0.25), residues: 1182
  helix:  0.93 (0.26), residues: 390
  sheet: -1.84 (0.30), residues: 286
  loop : -1.59 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B  82 
 HIS   0.004   0.001   HIS L  64 
 PHE   0.018   0.001   PHE R 111 
 TYR   0.020   0.001   TYR D 103 
 ARG   0.007   0.000   ARG B  68 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: A  256 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8361 (m110)
REVERT: A  324 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7768 (p)
REVERT: D   76 LYS cc_start: 0.7620 (pttt) cc_final: 0.7145 (tptp)
REVERT: D  103 TYR cc_start: 0.7661 (t80) cc_final: 0.7329 (t80)
REVERT: D  219 GLN cc_start: 0.8161 (pp30) cc_final: 0.7941 (pp30)
REVERT: L   56 GLN cc_start: 0.7975 (mp10) cc_final: 0.7462 (pm20)
REVERT: R  158 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7305 (tt)
  outliers start: 18
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1953
  time to fit residues: 38.6759
Evaluate side-chains
  129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  158 ILE
Chi-restraints excluded: chain R residue  279 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0010
   chunk 77 optimal weight:    0.0980
   chunk 39 optimal weight:    0.4980
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** L  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.091781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.073692 restraints weight = 24076.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.075912 restraints weight = 12239.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.076438 restraints weight = 7849.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9596  Z= 0.163
  Angle     :  0.602  10.010  13009  Z= 0.308
  Chirality :  0.043   0.209   1480
  Planarity :  0.003   0.047   1641
  Dihedral  :  4.457  43.158   1300
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.50 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.14 (0.25), residues: 1182
  helix:  1.01 (0.26), residues: 391
  sheet: -1.66 (0.31), residues: 276
  loop : -1.58 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.007   0.001   HIS L  64 
 PHE   0.017   0.001   PHE R 111 
 TYR   0.021   0.001   TYR D 103 
 ARG   0.005   0.000   ARG B  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3131.67 seconds
wall clock time: 55 minutes 16.03 seconds (3316.03 seconds total)