Starting phenix.real_space_refine
on Sun May 11 17:33:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y24_33585/05_2025/7y24_33585.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.075
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      57      5.16       5
     C    5251      2.51       5
     N    1381      2.21       5
     O    1540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8229
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1605
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 4, 'TRANS': 207}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 47
    Chain: "B"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2449
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 187
          Unresolved non-hydrogen dihedrals: 120
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 117
    Chain: "G"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 360
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "S"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1722
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 22
          Classifications: {'peptide': 3}
          Modifications used: {'PEPT-D': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'DPN%PEPT-D:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 4}
    Chain: "E"
      Number of atoms: 2027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2027
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 11, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 226
          Unresolved non-hydrogen angles: 272
          Unresolved non-hydrogen dihedrals: 197
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 97
  Time building chain proxies: 4.89, per 1000 atoms: 0.59
  Number of scatterers: 8229
  At special positions: 0
  Unit cell: (91.308, 120.657, 125.005, 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      57     16.00
     O    1540      8.00
     N    1381      7.00
     C    5251      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   2 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 115 " - pdb=" SG  CYS E 193 " 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
  Links applied
    TRANS
      " DTR C   4 " - " PHE C   3 "
  Time building additional restraints: 2.31
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DPN C   1 "
        pdb=" CB  DTR C   4 "
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 15 sheets defined
      37.2% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 4.471A  pdb=" N   THR A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.577A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 256
      removed outlier: 4.126A  pdb=" N   HIS A 245 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLU A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 280
      removed outlier: 4.306A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.695A  pdb=" N   VAL A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.784A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.930A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 72
    Processing helix  chain 'E' and resid 76 through 105
      Proline residue:  E  97  - end of helix
      removed outlier: 3.626A  pdb=" N   ALA E 100 " --> pdb=" O   LEU E  96 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN E 102 " --> pdb=" O   PHE E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 146
    Processing helix  chain 'E' and resid 146 through 154
    Processing helix  chain 'E' and resid 155 through 180
      Proline residue:  E 176  - end of helix
    Processing helix  chain 'E' and resid 203 through 219
    Processing helix  chain 'E' and resid 219 through 237
    Processing helix  chain 'E' and resid 244 through 282
      removed outlier: 4.438A  pdb=" N   LYS E 248 " --> pdb=" O   SER E 244 " (cutoff:3.500A)
      Proline residue:  E 271  - end of helix
    Processing helix  chain 'E' and resid 287 through 314
      Proline residue:  E 309  - end of helix
    Processing helix  chain 'E' and resid 316 through 325
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 9.228A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.953A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.870A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.676A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.573A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.635A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.738A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.315A  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: 3.869A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 5.256A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.583A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
    Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183
      removed outlier: 5.706A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL S 214 " --> pdb=" O   GLN S 167 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.619A  pdb=" N   PHE C   3 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR C   6 " --> pdb=" O   PHE C   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'E' and resid 182 through 185

    457 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1543
        1.33 -     1.45: 2200
        1.45 -     1.57: 4584
        1.57 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8405
  Sorted by residual:
  bond pdb=" N   LEU S 221 "
       pdb=" CA  LEU S 221 "
    ideal  model  delta    sigma   weight residual
    1.459  1.401  0.058 1.23e-02 6.61e+03 2.21e+01
  bond pdb=" N   TYR S 223 "
       pdb=" CA  TYR S 223 "
    ideal  model  delta    sigma   weight residual
    1.461  1.422  0.039 9.20e-03 1.18e+04 1.82e+01
  bond pdb=" CA  TYR S 223 "
       pdb=" C   TYR S 223 "
    ideal  model  delta    sigma   weight residual
    1.520  1.469  0.051 1.23e-02 6.61e+03 1.74e+01
  bond pdb=" CA  PRO S 224 "
       pdb=" CB  PRO S 224 "
    ideal  model  delta    sigma   weight residual
    1.532  1.481  0.051 1.33e-02 5.65e+03 1.49e+01
  bond pdb=" CA  LEU S 221 "
       pdb=" C   LEU S 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.482  0.042 1.29e-02 6.01e+03 1.04e+01
  ... (remaining 8400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 11331
        2.53 -     5.05: 121
        5.05 -     7.58: 12
        7.58 -    10.11: 2
       10.11 -    12.64: 2
  Bond angle restraints: 11468
  Sorted by residual:
  angle pdb=" N   TYR S 223 "
        pdb=" CA  TYR S 223 "
        pdb=" C   TYR S 223 "
      ideal   model   delta    sigma   weight residual
     112.75  125.39  -12.64 1.36e+00 5.41e-01 8.63e+01
  angle pdb=" CA  TYR S 223 "
        pdb=" CB  TYR S 223 "
        pdb=" CG  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     113.90  103.75   10.15 1.80e+00 3.09e-01 3.18e+01
  angle pdb=" O   TYR S 223 "
        pdb=" C   TYR S 223 "
        pdb=" N   PRO S 224 "
      ideal   model   delta    sigma   weight residual
     120.48  124.22   -3.74 8.90e-01 1.26e+00 1.76e+01
  angle pdb=" N   PRO S 224 "
        pdb=" CA  PRO S 224 "
        pdb=" C   PRO S 224 "
      ideal   model   delta    sigma   weight residual
     111.03  105.02    6.01 1.54e+00 4.22e-01 1.52e+01
  angle pdb=" C   GLU S 222 "
        pdb=" N   TYR S 223 "
        pdb=" CA  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     120.26  115.51    4.75 1.34e+00 5.57e-01 1.25e+01
  ... (remaining 11463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4513
       17.95 -    35.91: 305
       35.91 -    53.86: 55
       53.86 -    71.81: 12
       71.81 -    89.77: 5
  Dihedral angle restraints: 4890
    sinusoidal: 1628
      harmonic: 3262
  Sorted by residual:
  dihedral pdb=" N   TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" CA  TYR S 223 "
           pdb=" CB  TYR S 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  147.56  -24.76     0      2.50e+00 1.60e-01 9.81e+01
  dihedral pdb=" C   TYR S 223 "
           pdb=" N   TYR S 223 "
           pdb=" CA  TYR S 223 "
           pdb=" CB  TYR S 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -146.50   23.90     0      2.50e+00 1.60e-01 9.14e+01
  dihedral pdb=" CB  CYS E 115 "
           pdb=" SG  CYS E 115 "
           pdb=" SG  CYS E 193 "
           pdb=" CB  CYS E 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.61  -86.61     1      1.00e+01 1.00e-02 9.03e+01
  ... (remaining 4887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.247: 1353
       0.247 -    0.494: 0
       0.494 -    0.740: 1
       0.740 -    0.987: 0
       0.987 -    1.234: 1
  Chirality restraints: 1355
  Sorted by residual:
  chirality pdb=" CA  TYR S 223 "
            pdb=" N   TYR S 223 "
            pdb=" C   TYR S 223 "
            pdb=" CB  TYR S 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.28    1.23 2.00e-01 2.50e+01 3.81e+01
  chirality pdb=" CA  GLU S 222 "
            pdb=" N   GLU S 222 "
            pdb=" C   GLU S 222 "
            pdb=" CB  GLU S 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.18e+00
  chirality pdb=" CA  LEU S 221 "
            pdb=" N   LEU S 221 "
            pdb=" C   LEU S 221 "
            pdb=" CB  LEU S 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.13e-01
  ... (remaining 1352 not shown)

  Planarity restraints: 1453
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR S 223 "    0.018 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   TYR S 223 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   TYR S 223 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO S 224 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 223 "    0.033 2.00e-02 2.50e+03   2.22e-02 9.89e+00
        pdb=" CG  TYR S 223 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 223 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 223 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 223 "    0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 223 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 223 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR S 223 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 164 "    0.018 2.00e-02 2.50e+03   1.52e-02 5.80e+00
        pdb=" CG  TRP S 164 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 164 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 164 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 164 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 164 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 164 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 164 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 164 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 164 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1450 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 886
        2.75 -     3.29: 8456
        3.29 -     3.82: 14065
        3.82 -     4.36: 15802
        4.36 -     4.90: 27828
  Nonbonded interactions: 67037
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OE2 GLU A   9 "
            pdb=" ND2 ASN S 157 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   SER S  52 "
            pdb=" NH1 ARG S  72 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   ASP B 228 "
            pdb=" OG  SER B 245 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.255 3.040
  ... (remaining 67032 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.550
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
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   0.058   8409  Z= 0.204
  Angle     :  0.676  12.637  11477  Z= 0.383
  Chirality :  0.057   1.234   1355
  Planarity :  0.005   0.055   1452
  Dihedral  : 12.927  89.767   2776
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  0.25 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1107
  helix:  1.98 (0.26), residues: 389
  sheet: -0.01 (0.30), residues: 279
  loop : -0.56 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP S 164 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.026   0.002   PHE E  92 
 TYR   0.045   0.002   TYR S 223 
 ARG   0.009   0.001   ARG S  18 

Details of bonding type rmsd
  link_TRANS           : bond        0.00014 (    1)
  link_TRANS           : angle       0.05916 (    3)
  hydrogen bonds       : bond        0.12097 (  457)
  hydrogen bonds       : angle       5.82478 ( 1323)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       1.81877 (    6)
  covalent geometry    : bond        0.00370 ( 8405)
  covalent geometry    : angle       0.67517 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: A  305 GLN cc_start: 0.8572 (mt0) cc_final: 0.8117 (tm-30)
REVERT: A  313 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8278 (ttm110)
REVERT: A  322 HIS cc_start: 0.7067 (t-90) cc_final: 0.6677 (t-90)
REVERT: G   40 TYR cc_start: 0.7716 (t80) cc_final: 0.7312 (t80)
REVERT: S  148 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6284 (ttp80)
REVERT: S  218 MET cc_start: 0.6506 (mtp) cc_final: 0.6271 (mtp)
REVERT: S  222 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8305 (mm-30)
REVERT: E  122 ASP cc_start: 0.7856 (t70) cc_final: 0.7413 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 221
  average time/residue: 0.1756
  time to fit residues: 54.0173
Evaluate side-chains
  189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain S residue  222 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 259 GLN
S 182 ASN
E 308 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.182411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.140954 restraints weight = 11457.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 3.30
r_work: 0.3637 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8409  Z= 0.135
  Angle     :  0.567   6.403  11477  Z= 0.302
  Chirality :  0.043   0.201   1355
  Planarity :  0.004   0.053   1452
  Dihedral  :  4.751  59.182   1204
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  9.98 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1107
  helix:  2.25 (0.25), residues: 393
  sheet: -0.01 (0.30), residues: 281
  loop : -0.66 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 153 
 HIS   0.005   0.001   HIS E 107 
 PHE   0.020   0.002   PHE E  92 
 TYR   0.023   0.001   TYR S 223 
 ARG   0.004   0.001   ARG S  98 

Details of bonding type rmsd
  link_TRANS           : bond        0.00080 (    1)
  link_TRANS           : angle       0.15224 (    3)
  hydrogen bonds       : bond        0.03945 (  457)
  hydrogen bonds       : angle       4.80598 ( 1323)
  SS BOND              : bond        0.00118 (    3)
  SS BOND              : angle       1.13460 (    6)
  covalent geometry    : bond        0.00303 ( 8405)
  covalent geometry    : angle       0.56623 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 GLN cc_start: 0.8516 (mt0) cc_final: 0.7972 (tm-30)
REVERT: A  313 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8599 (ttm110)
REVERT: A  341 ASP cc_start: 0.8515 (t0) cc_final: 0.7985 (m-30)
REVERT: B  101 MET cc_start: 0.8697 (mtp) cc_final: 0.8383 (mtp)
REVERT: S  182 ASN cc_start: 0.7497 (m-40) cc_final: 0.7296 (m110)
REVERT: S  218 MET cc_start: 0.6490 (mtp) cc_final: 0.6209 (mtp)
  outliers start: 23
  outliers final: 16
  residues processed: 223
  average time/residue: 0.1773
  time to fit residues: 55.2354
Evaluate side-chains
  213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  172 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  227 CYS
Chi-restraints excluded: chain E residue  308 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    0.0020
   chunk 14 optimal weight:    8.9990
   chunk 81 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 79 optimal weight:   20.0000
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
S  35 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.182350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.141137 restraints weight = 11619.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 3.31
r_work: 0.3636 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8409  Z= 0.121
  Angle     :  0.547   5.641  11477  Z= 0.293
  Chirality :  0.042   0.167   1355
  Planarity :  0.004   0.049   1452
  Dihedral  :  4.127  23.885   1199
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.79 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1107
  helix:  2.16 (0.25), residues: 400
  sheet:  0.03 (0.30), residues: 286
  loop : -0.61 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 197 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.019   0.001   PHE E  92 
 TYR   0.025   0.001   TYR S 223 
 ARG   0.003   0.000   ARG B  49 

Details of bonding type rmsd
  link_TRANS           : bond        0.00065 (    1)
  link_TRANS           : angle       0.23216 (    3)
  hydrogen bonds       : bond        0.03637 (  457)
  hydrogen bonds       : angle       4.69551 ( 1323)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       1.85964 (    6)
  covalent geometry    : bond        0.00267 ( 8405)
  covalent geometry    : angle       0.54532 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 GLN cc_start: 0.8546 (mt0) cc_final: 0.7978 (tm-30)
REVERT: A  333 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: A  337 ASP cc_start: 0.9006 (m-30) cc_final: 0.8773 (m-30)
REVERT: A  341 ASP cc_start: 0.8562 (t0) cc_final: 0.8000 (m-30)
REVERT: B  153 ASP cc_start: 0.7299 (m-30) cc_final: 0.7078 (m-30)
REVERT: S  223 TYR cc_start: 0.7277 (t80) cc_final: 0.6997 (t80)
REVERT: E   92 PHE cc_start: 0.8096 (t80) cc_final: 0.7707 (t80)
REVERT: E  139 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7672 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 207
  average time/residue: 0.1712
  time to fit residues: 50.2269
Evaluate side-chains
  201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  172 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  225 LEU
Chi-restraints excluded: chain E residue  139 ASP
Chi-restraints excluded: chain E residue  227 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.181407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139923 restraints weight = 11553.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 3.29
r_work: 0.3622 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8409  Z= 0.125
  Angle     :  0.542   6.974  11477  Z= 0.290
  Chirality :  0.042   0.184   1355
  Planarity :  0.004   0.048   1452
  Dihedral  :  4.015  22.742   1199
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.64 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.25), residues: 1107
  helix:  2.14 (0.25), residues: 401
  sheet: -0.05 (0.30), residues: 290
  loop : -0.59 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 197 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.018   0.001   PHE E  92 
 TYR   0.021   0.001   TYR S 223 
 ARG   0.003   0.000   ARG E 184 

Details of bonding type rmsd
  link_TRANS           : bond        0.00051 (    1)
  link_TRANS           : angle       0.15484 (    3)
  hydrogen bonds       : bond        0.03520 (  457)
  hydrogen bonds       : angle       4.54290 ( 1323)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.22234 (    6)
  covalent geometry    : bond        0.00282 ( 8405)
  covalent geometry    : angle       0.54171 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 GLN cc_start: 0.8561 (mt0) cc_final: 0.7980 (tm-30)
REVERT: A  333 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7502 (tm-30)
REVERT: A  337 ASP cc_start: 0.8868 (m-30) cc_final: 0.8575 (m-30)
REVERT: B  153 ASP cc_start: 0.7283 (m-30) cc_final: 0.7054 (m-30)
REVERT: B  198 LEU cc_start: 0.8138 (mm) cc_final: 0.7843 (pt)
REVERT: B  325 MET cc_start: 0.7714 (ttm) cc_final: 0.7304 (ttt)
REVERT: S   12 VAL cc_start: 0.3764 (OUTLIER) cc_final: 0.3179 (m)
REVERT: S  148 ARG cc_start: 0.6728 (ttp80) cc_final: 0.6505 (ttp80)
REVERT: S  223 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: E  139 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7698 (t0)
  outliers start: 27
  outliers final: 16
  residues processed: 214
  average time/residue: 0.1926
  time to fit residues: 56.8991
Evaluate side-chains
  202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   59 CYS
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  139 ASP
Chi-restraints excluded: chain E residue  213 PHE
Chi-restraints excluded: chain E residue  227 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 102 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 23 optimal weight:   30.0000
   chunk 105 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.174711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.132438 restraints weight = 11948.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 3.19
r_work: 0.3551 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.080   8409  Z= 0.321
  Angle     :  0.729  10.366  11477  Z= 0.390
  Chirality :  0.049   0.203   1355
  Planarity :  0.005   0.055   1452
  Dihedral  :  4.653  24.967   1199
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 16.87 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1107
  helix:  1.46 (0.25), residues: 397
  sheet: -0.22 (0.29), residues: 298
  loop : -0.75 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 212 
 HIS   0.012   0.002   HIS B  91 
 PHE   0.030   0.003   PHE E  92 
 TYR   0.020   0.002   TYR E 302 
 ARG   0.006   0.001   ARG A  15 

Details of bonding type rmsd
  link_TRANS           : bond        0.00109 (    1)
  link_TRANS           : angle       0.28702 (    3)
  hydrogen bonds       : bond        0.04921 (  457)
  hydrogen bonds       : angle       5.11825 ( 1323)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       1.68191 (    6)
  covalent geometry    : bond        0.00753 ( 8405)
  covalent geometry    : angle       0.72875 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 196
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8600 (mp0) cc_final: 0.8314 (mp0)
REVERT: A  187 GLU cc_start: 0.7579 (tt0) cc_final: 0.7299 (tt0)
REVERT: A  305 GLN cc_start: 0.8619 (mt0) cc_final: 0.7985 (tm-30)
REVERT: A  313 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8612 (ttp-110)
REVERT: A  322 HIS cc_start: 0.7936 (t-90) cc_final: 0.7553 (t-90)
REVERT: A  333 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8061 (tp40)
REVERT: B  325 MET cc_start: 0.8280 (ttm) cc_final: 0.7924 (ttt)
REVERT: S   36 TRP cc_start: 0.7916 (m100) cc_final: 0.7649 (m100)
REVERT: S  223 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.7108 (t80)
REVERT: E  139 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7757 (t0)
  outliers start: 41
  outliers final: 27
  residues processed: 222
  average time/residue: 0.1782
  time to fit residues: 55.2140
Evaluate side-chains
  213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  172 SER
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   59 CYS
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  139 ASP
Chi-restraints excluded: chain E residue  174 ILE
Chi-restraints excluded: chain E residue  213 PHE
Chi-restraints excluded: chain E residue  227 CYS
Chi-restraints excluded: chain E residue  231 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0970
   chunk 101 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.173116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.130248 restraints weight = 11638.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 3.28
r_work: 0.3506 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8409  Z= 0.180
  Angle     :  0.612   8.261  11477  Z= 0.326
  Chirality :  0.044   0.190   1355
  Planarity :  0.004   0.056   1452
  Dihedral  :  4.445  26.543   1199
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 18.72 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1107
  helix:  1.70 (0.25), residues: 398
  sheet: -0.32 (0.29), residues: 301
  loop : -0.63 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 197 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.040   0.002   PHE E  92 
 TYR   0.028   0.002   TYR E 273 
 ARG   0.005   0.000   ARG B 251 

Details of bonding type rmsd
  link_TRANS           : bond        0.00051 (    1)
  link_TRANS           : angle       0.12765 (    3)
  hydrogen bonds       : bond        0.04107 (  457)
  hydrogen bonds       : angle       4.86796 ( 1323)
  SS BOND              : bond        0.00129 (    3)
  SS BOND              : angle       0.99660 (    6)
  covalent geometry    : bond        0.00421 ( 8405)
  covalent geometry    : angle       0.61142 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 197
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8536 (mp0) cc_final: 0.8097 (mp0)
REVERT: A  187 GLU cc_start: 0.7725 (tt0) cc_final: 0.7467 (tt0)
REVERT: A  313 ARG cc_start: 0.8975 (ttp-170) cc_final: 0.8754 (ttm110)
REVERT: A  322 HIS cc_start: 0.7645 (t-90) cc_final: 0.7237 (t-90)
REVERT: A  333 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8330 (tp40)
REVERT: B  283 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7638 (tpt170)
REVERT: B  325 MET cc_start: 0.8246 (ttm) cc_final: 0.7836 (ttt)
REVERT: S   12 VAL cc_start: 0.3664 (OUTLIER) cc_final: 0.3015 (m)
REVERT: S   36 TRP cc_start: 0.7842 (m100) cc_final: 0.7617 (m100)
REVERT: S  113 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7910 (mm-40)
REVERT: S  148 ARG cc_start: 0.6929 (ttp80) cc_final: 0.6461 (ttp80)
REVERT: S  223 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6899 (t80)
REVERT: E  139 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (t0)
  outliers start: 39
  outliers final: 28
  residues processed: 223
  average time/residue: 0.1824
  time to fit residues: 56.3204
Evaluate side-chains
  219 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  172 SER
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  122 ASP
Chi-restraints excluded: chain E residue  139 ASP
Chi-restraints excluded: chain E residue  174 ILE
Chi-restraints excluded: chain E residue  227 CYS
Chi-restraints excluded: chain E residue  297 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 108 optimal weight:    0.3980
   chunk 107 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.174627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132283 restraints weight = 11588.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 3.27
r_work: 0.3533 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8409  Z= 0.150
  Angle     :  0.599   7.663  11477  Z= 0.318
  Chirality :  0.043   0.190   1355
  Planarity :  0.004   0.056   1452
  Dihedral  :  4.333  26.342   1199
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.44 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1107
  helix:  1.90 (0.26), residues: 392
  sheet: -0.29 (0.29), residues: 291
  loop : -0.64 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 212 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.029   0.002   PHE E  92 
 TYR   0.022   0.001   TYR E 302 
 ARG   0.004   0.000   ARG S 168 

Details of bonding type rmsd
  link_TRANS           : bond        0.00041 (    1)
  link_TRANS           : angle       0.15070 (    3)
  hydrogen bonds       : bond        0.03910 (  457)
  hydrogen bonds       : angle       4.81903 ( 1323)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       1.88316 (    6)
  covalent geometry    : bond        0.00347 ( 8405)
  covalent geometry    : angle       0.59807 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8538 (mp0) cc_final: 0.8072 (mp0)
REVERT: A  313 ARG cc_start: 0.8980 (ttp-170) cc_final: 0.8772 (ttm110)
REVERT: A  322 HIS cc_start: 0.7616 (t-90) cc_final: 0.7200 (t-90)
REVERT: B  153 ASP cc_start: 0.7278 (m-30) cc_final: 0.7074 (m-30)
REVERT: B  325 MET cc_start: 0.8214 (ttm) cc_final: 0.7909 (ttt)
REVERT: S   12 VAL cc_start: 0.3766 (OUTLIER) cc_final: 0.3121 (m)
REVERT: S   19 LYS cc_start: 0.8291 (ttpp) cc_final: 0.8071 (ttpp)
REVERT: S   36 TRP cc_start: 0.7823 (m100) cc_final: 0.7542 (m100)
REVERT: S  148 ARG cc_start: 0.6755 (ttp80) cc_final: 0.6534 (ttp80)
REVERT: S  223 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6938 (t80)
REVERT: E   93 MET cc_start: 0.8582 (mmm) cc_final: 0.7954 (mmm)
  outliers start: 32
  outliers final: 27
  residues processed: 215
  average time/residue: 0.1776
  time to fit residues: 53.6561
Evaluate side-chains
  220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  172 SER
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  122 ASP
Chi-restraints excluded: chain E residue  174 ILE
Chi-restraints excluded: chain E residue  229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.177768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135793 restraints weight = 11623.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 3.29
r_work: 0.3580 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8409  Z= 0.126
  Angle     :  0.573   7.373  11477  Z= 0.304
  Chirality :  0.042   0.179   1355
  Planarity :  0.004   0.056   1452
  Dihedral  :  4.127  25.176   1199
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.80 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1107
  helix:  2.05 (0.26), residues: 391
  sheet: -0.22 (0.30), residues: 288
  loop : -0.62 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 212 
 HIS   0.003   0.001   HIS E 107 
 PHE   0.033   0.002   PHE E  92 
 TYR   0.018   0.001   TYR S 223 
 ARG   0.004   0.000   ARG E 184 

Details of bonding type rmsd
  link_TRANS           : bond        0.00012 (    1)
  link_TRANS           : angle       0.13474 (    3)
  hydrogen bonds       : bond        0.03620 (  457)
  hydrogen bonds       : angle       4.69900 ( 1323)
  SS BOND              : bond        0.00112 (    3)
  SS BOND              : angle       1.83186 (    6)
  covalent geometry    : bond        0.00290 ( 8405)
  covalent geometry    : angle       0.57189 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8517 (mp0) cc_final: 0.8049 (mp0)
REVERT: A  187 GLU cc_start: 0.7467 (tt0) cc_final: 0.7248 (tt0)
REVERT: A  322 HIS cc_start: 0.7692 (t-90) cc_final: 0.7219 (t-90)
REVERT: A  333 GLN cc_start: 0.8372 (tp40) cc_final: 0.8109 (tp40)
REVERT: B  325 MET cc_start: 0.8061 (ttm) cc_final: 0.7776 (ttt)
REVERT: S   12 VAL cc_start: 0.3760 (OUTLIER) cc_final: 0.3127 (m)
REVERT: S   19 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8081 (ttpp)
REVERT: S   35 HIS cc_start: 0.8951 (m90) cc_final: 0.8618 (m-70)
REVERT: S   36 TRP cc_start: 0.7726 (m100) cc_final: 0.7468 (m100)
REVERT: S  220 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7489 (t-90)
REVERT: E   92 PHE cc_start: 0.8321 (t80) cc_final: 0.7718 (t80)
REVERT: E  257 MET cc_start: 0.7086 (mmt) cc_final: 0.6814 (mmt)
  outliers start: 25
  outliers final: 21
  residues processed: 227
  average time/residue: 0.1871
  time to fit residues: 60.0501
Evaluate side-chains
  221 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  174 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    0.0050
   chunk 71 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 41 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 47 optimal weight:    9.9990
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.177545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.135381 restraints weight = 11712.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 3.31
r_work: 0.3570 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8409  Z= 0.138
  Angle     :  0.606   9.646  11477  Z= 0.319
  Chirality :  0.043   0.181   1355
  Planarity :  0.004   0.057   1452
  Dihedral  :  4.178  26.417   1199
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.80 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1107
  helix:  2.03 (0.26), residues: 391
  sheet: -0.21 (0.30), residues: 288
  loop : -0.60 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 212 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.030   0.002   PHE E  92 
 TYR   0.045   0.002   TYR S 223 
 ARG   0.004   0.000   ARG B 251 

Details of bonding type rmsd
  link_TRANS           : bond        0.00022 (    1)
  link_TRANS           : angle       0.17565 (    3)
  hydrogen bonds       : bond        0.03657 (  457)
  hydrogen bonds       : angle       4.73966 ( 1323)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       1.59464 (    6)
  covalent geometry    : bond        0.00318 ( 8405)
  covalent geometry    : angle       0.60550 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8520 (mp0) cc_final: 0.8047 (mp0)
REVERT: A  322 HIS cc_start: 0.7683 (t-90) cc_final: 0.7193 (t-90)
REVERT: B  325 MET cc_start: 0.8117 (ttm) cc_final: 0.7820 (ttt)
REVERT: S   12 VAL cc_start: 0.3749 (OUTLIER) cc_final: 0.3105 (m)
REVERT: S   36 TRP cc_start: 0.7793 (m100) cc_final: 0.7566 (m100)
REVERT: E   92 PHE cc_start: 0.8348 (t80) cc_final: 0.7956 (t80)
REVERT: E  257 MET cc_start: 0.6900 (mmt) cc_final: 0.6673 (mmt)
  outliers start: 28
  outliers final: 24
  residues processed: 212
  average time/residue: 0.1802
  time to fit residues: 53.2286
Evaluate side-chains
  212 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  122 ASP
Chi-restraints excluded: chain E residue  174 ILE
Chi-restraints excluded: chain E residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 88 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.183013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.147574 restraints weight = 11890.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 3.47
r_work: 0.3733 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8409  Z= 0.143
  Angle     :  0.638  14.194  11477  Z= 0.328
  Chirality :  0.043   0.185   1355
  Planarity :  0.004   0.057   1452
  Dihedral  :  4.180  26.297   1199
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.15 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1107
  helix:  2.01 (0.26), residues: 390
  sheet: -0.21 (0.29), residues: 288
  loop : -0.60 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 212 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.030   0.002   PHE E  92 
 TYR   0.035   0.002   TYR S 223 
 ARG   0.005   0.000   ARG B 251 

Details of bonding type rmsd
  link_TRANS           : bond        0.00023 (    1)
  link_TRANS           : angle       0.17300 (    3)
  hydrogen bonds       : bond        0.03644 (  457)
  hydrogen bonds       : angle       4.74571 ( 1323)
  SS BOND              : bond        0.00092 (    3)
  SS BOND              : angle       1.41664 (    6)
  covalent geometry    : bond        0.00335 ( 8405)
  covalent geometry    : angle       0.63745 (11468)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8530 (mp0) cc_final: 0.8181 (mp0)
REVERT: A  322 HIS cc_start: 0.7750 (t-90) cc_final: 0.7328 (t-90)
REVERT: B  325 MET cc_start: 0.7999 (ttm) cc_final: 0.7772 (ttt)
REVERT: G   40 TYR cc_start: 0.8011 (t80) cc_final: 0.7592 (t80)
REVERT: S   36 TRP cc_start: 0.7900 (m100) cc_final: 0.7622 (m100)
REVERT: E   92 PHE cc_start: 0.8366 (t80) cc_final: 0.7975 (t80)
REVERT: E  257 MET cc_start: 0.6830 (mmt) cc_final: 0.6619 (mmt)
  outliers start: 24
  outliers final: 24
  residues processed: 203
  average time/residue: 0.1850
  time to fit residues: 52.1015
Evaluate side-chains
  211 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  174 ILE
Chi-restraints excluded: chain E residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 103 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.184062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.148259 restraints weight = 12089.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 3.26
r_work: 0.3691 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8409  Z= 0.145
  Angle     :  0.635  11.055  11477  Z= 0.330
  Chirality :  0.044   0.247   1355
  Planarity :  0.004   0.057   1452
  Dihedral  :  4.165  26.508   1199
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.03 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1107
  helix:  1.98 (0.26), residues: 390
  sheet: -0.22 (0.30), residues: 288
  loop : -0.61 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 212 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.031   0.002   PHE E  92 
 TYR   0.036   0.002   TYR S 223 
 ARG   0.005   0.001   ARG S 148 

Details of bonding type rmsd
  link_TRANS           : bond        0.00028 (    1)
  link_TRANS           : angle       0.18247 (    3)
  hydrogen bonds       : bond        0.03696 (  457)
  hydrogen bonds       : angle       4.74373 ( 1323)
  SS BOND              : bond        0.00064 (    3)
  SS BOND              : angle       1.51059 (    6)
  covalent geometry    : bond        0.00339 ( 8405)
  covalent geometry    : angle       0.63386 (11468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5077.39 seconds
wall clock time: 88 minutes 15.64 seconds (5295.64 seconds total)