Starting phenix.real_space_refine
on Wed Feb  4 04:51:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kwx_62619/02_2026/9kwx_62619.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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    5547      2.51       5
     N    1491      2.21       5
     O    1591      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8686
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2199
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 14, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 5, 'PHE:plan': 1, 'TYR:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "B"
      Number of atoms: 1544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1544
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 4, 'TRANS': 204}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 140
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 74
    Chain: "C"
      Number of atoms: 2491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2491
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASP:plan': 6, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 87
    Chain: "G"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 376
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "H"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1657
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "F"
      Number of atoms: 419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 419
          Classifications: {'peptide': 67}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 3, 'TRANS': 63}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 105
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 71
  Time building chain proxies: 1.59, per 1000 atoms: 0.18
  Number of scatterers: 8686
  At special positions: 0
  Unit cell: (91.874, 119.048, 146.222, 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    1591      8.00
     N    1491      7.00
     C    5547      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  21 " - pdb=" SG  CYS F  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  34 " - pdb=" SG  CYS F  55 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 275.6 milliseconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2222

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      38.0% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 39
    Processing helix  chain 'A' and resid 40 through 61
      removed outlier: 3.968A  pdb=" N   VAL A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      Proline residue:  A  53  - end of helix
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 71 through 98
      removed outlier: 4.515A  pdb=" N   PHE A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
      Proline residue:  A  90  - end of helix
    Processing helix  chain 'A' and resid 105 through 110
    Processing helix  chain 'A' and resid 111 through 140
      removed outlier: 3.775A  pdb=" N   VAL A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 173
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 200 through 231
      removed outlier: 3.506A  pdb=" N   LEU A 206 " --> pdb=" O   ALA A 202 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   LEU A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
      removed outlier: 3.634A  pdb=" N   PHE A 225 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 269
      removed outlier: 3.611A  pdb=" N   LEU A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
      Proline residue:  A 258  - end of helix
      removed outlier: 3.767A  pdb=" N   ALA A 267 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 305
      removed outlier: 3.878A  pdb=" N   VAL A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   SER A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU A 285 " --> pdb=" O   LYS A 281 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   CYS A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      Proline residue:  A 298  - end of helix
      removed outlier: 3.693A  pdb=" N   TYR A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'B' and resid 9 through 31
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 4.156A  pdb=" N   VAL B  50 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 205
    Processing helix  chain 'B' and resid 208 through 217
      removed outlier: 4.680A  pdb=" N   ILE B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   HIS B 214 " --> pdb=" O   LYS B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 256
    Processing helix  chain 'B' and resid 271 through 280
      removed outlier: 3.766A  pdb=" N   GLY B 276 " --> pdb=" O   LYS B 272 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLU B 277 " --> pdb=" O   ASP B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 296 through 310
    Processing helix  chain 'B' and resid 330 through 351
    Processing helix  chain 'C' and resid 4 through 26
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 4.023A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.931A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.600A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 4.002A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 11
    Processing helix  chain 'F' and resid 15 through 25
    Processing helix  chain 'F' and resid 47 through 64
      removed outlier: 4.623A  pdb=" N   GLU F  53 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178
    Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 192
    Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227
      removed outlier: 6.481A  pdb=" N   VAL B 226 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.542A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.801A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105
      removed outlier: 3.796A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153
      removed outlier: 6.446A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.811A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.579A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.524A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ASN C 293 " --> pdb=" O   TYR C 289 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.691A  pdb=" N   VAL H   5 " --> pdb=" O   SER H  23 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.222A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.222A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 142
    Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148
      removed outlier: 6.369A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2812
        1.34 -     1.46: 2144
        1.46 -     1.58: 3837
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8866
  Sorted by residual:
  bond pdb=" C   SER F  65 "
       pdb=" N   PRO F  66 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.018 8.40e-03 1.42e+04 4.49e+00
  bond pdb=" N   ASP H   1 "
       pdb=" CA  ASP H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  bond pdb=" N   GLU C   3 "
       pdb=" CA  GLU C   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  bond pdb=" N   LEU B   5 "
       pdb=" CA  LEU B   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.77e+00
  bond pdb=" N   ALA G   7 "
       pdb=" CA  ALA G   7 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.76e+00
  ... (remaining 8861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 11381
        1.31 -     2.63: 583
        2.63 -     3.94: 107
        3.94 -     5.25: 21
        5.25 -     6.57: 3
  Bond angle restraints: 12095
  Sorted by residual:
  angle pdb=" N   PHE A 308 "
        pdb=" CA  PHE A 308 "
        pdb=" CB  PHE A 308 "
      ideal   model   delta    sigma   weight residual
     114.17  109.49    4.68 1.14e+00 7.69e-01 1.68e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.49   -5.95 1.91e+00 2.74e-01 9.69e+00
  angle pdb=" N   GLN A 306 "
        pdb=" CA  GLN A 306 "
        pdb=" C   GLN A 306 "
      ideal   model   delta    sigma   weight residual
     112.57  109.07    3.50 1.13e+00 7.83e-01 9.59e+00
  angle pdb=" N   VAL B 219 "
        pdb=" CA  VAL B 219 "
        pdb=" C   VAL B 219 "
      ideal   model   delta    sigma   weight residual
     110.05  106.72    3.33 1.09e+00 8.42e-01 9.35e+00
  angle pdb=" N   THR B 329 "
        pdb=" CA  THR B 329 "
        pdb=" CB  THR B 329 "
      ideal   model   delta    sigma   weight residual
     114.17  110.76    3.41 1.14e+00 7.69e-01 8.95e+00
  ... (remaining 12090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 4874
       17.00 -    34.00: 266
       34.00 -    51.00: 43
       51.00 -    68.00: 8
       68.00 -    85.00: 3
  Dihedral angle restraints: 5194
    sinusoidal: 1756
      harmonic: 3438
  Sorted by residual:
  dihedral pdb=" CB  CYS H 159 "
           pdb=" SG  CYS H 159 "
           pdb=" SG  CYS H 229 "
           pdb=" CB  CYS H 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.27  -49.27     1      1.00e+01 1.00e-02 3.34e+01
  dihedral pdb=" CA  TRP A 143 "
           pdb=" C   TRP A 143 "
           pdb=" N   CYS A 144 "
           pdb=" CA  CYS A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.88   25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  CYS F  47 "
           pdb=" C   CYS F  47 "
           pdb=" N   ILE F  48 "
           pdb=" CA  ILE F  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.24  -24.76     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 5191 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 896
       0.033 -    0.066: 379
       0.066 -    0.099: 109
       0.099 -    0.132: 51
       0.132 -    0.166: 5
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ILE C 232 "
            pdb=" N   ILE C 232 "
            pdb=" C   ILE C 232 "
            pdb=" CB  ILE C 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.85e-01
  chirality pdb=" CA  ILE H 189 "
            pdb=" N   ILE H 189 "
            pdb=" C   ILE H 189 "
            pdb=" CB  ILE H 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  PRO C 236 "
            pdb=" N   PRO C 236 "
            pdb=" C   PRO C 236 "
            pdb=" CB  PRO C 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.24e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  65 "    0.047 5.00e-02 4.00e+02   7.21e-02 8.33e+00
        pdb=" N   PRO F  66 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO F  66 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO F  66 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  68 "    0.041 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO F  69 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO F  69 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F  69 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 209 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.20e+00
        pdb=" C   MET A 209 "    0.039 2.00e-02 2.50e+03
        pdb=" O   MET A 209 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 210 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1528 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 2597
        2.82 -     3.34: 8566
        3.34 -     3.86: 13959
        3.86 -     4.38: 16882
        4.38 -     4.90: 29039
  Nonbonded interactions: 71043
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 100 "
            pdb=" OE1 GLN F  71 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   ASP C 333 "
            pdb=" OG  SER C 334 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR C  65 "
            pdb=" O   PRO C 107 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OE1 GLN H 142 "
            pdb=" N   GLY H 242 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" O   ASP C 212 "
            pdb=" OD1 ASP C 212 "
     model   vdw
     2.401 3.040
  ... (remaining 71038 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:             1.160
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.530
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
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      :  0.003   0.039   8872  Z= 0.152
  Angle     :  0.685   6.566  12107  Z= 0.387
  Chirality :  0.043   0.166   1440
  Planarity :  0.006   0.072   1531
  Dihedral  : 11.335  85.000   2954
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.24), residues: 1168
  helix:  0.01 (0.25), residues: 425
  sheet: -0.49 (0.30), residues: 265
  loop : -0.98 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 180 
 TYR   0.019   0.002   TYR A  44 
 PHE   0.017   0.002   PHE C 292 
 TRP   0.019   0.002   TRP A  60 
 HIS   0.020   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8866)
  covalent geometry    : angle       0.68452 (12095)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       1.18873 (   12)
  hydrogen bonds       : bond        0.15552 (  444)
  hydrogen bonds       : angle       7.39362 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 TRP cc_start: 0.7073 (m100) cc_final: 0.6539 (m100)
REVERT: A   93 PHE cc_start: 0.7297 (t80) cc_final: 0.6895 (t80)
REVERT: A  120 MET cc_start: 0.6423 (mtt) cc_final: 0.6200 (mtp)
REVERT: A  134 ARG cc_start: 0.6865 (mtm180) cc_final: 0.6539 (mtp180)
REVERT: A  205 ILE cc_start: 0.8181 (tp) cc_final: 0.7954 (tp)
REVERT: A  231 TRP cc_start: 0.8074 (m100) cc_final: 0.7859 (m100)
REVERT: A  243 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7565 (mtmm)
REVERT: A  252 PHE cc_start: 0.7782 (t80) cc_final: 0.7546 (t80)
REVERT: B  189 HIS cc_start: 0.7462 (p-80) cc_final: 0.6946 (p-80)
REVERT: B  272 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7360 (ttpp)
REVERT: B  303 TYR cc_start: 0.8256 (t80) cc_final: 0.7842 (t80)
REVERT: B  305 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: B  330 ASN cc_start: 0.7472 (t0) cc_final: 0.7016 (t0)
REVERT: B  346 ASN cc_start: 0.7960 (m-40) cc_final: 0.7721 (m-40)
REVERT: C   35 ASN cc_start: 0.7716 (t0) cc_final: 0.7328 (p0)
REVERT: C   42 ARG cc_start: 0.6996 (ttt-90) cc_final: 0.6791 (ttt-90)
REVERT: C   88 ASN cc_start: 0.8244 (m-40) cc_final: 0.7993 (m110)
REVERT: C  124 TYR cc_start: 0.8369 (m-80) cc_final: 0.7724 (m-80)
REVERT: C  128 THR cc_start: 0.7979 (m) cc_final: 0.7227 (t)
REVERT: C  129 ARG cc_start: 0.6767 (ttp-110) cc_final: 0.6552 (ttt90)
REVERT: C  173 THR cc_start: 0.8560 (m) cc_final: 0.8090 (t)
REVERT: C  195 ASP cc_start: 0.7758 (p0) cc_final: 0.7555 (p0)
REVERT: C  227 SER cc_start: 0.8462 (t) cc_final: 0.8074 (m)
REVERT: C  263 THR cc_start: 0.7496 (m) cc_final: 0.7201 (p)
REVERT: C  274 THR cc_start: 0.8349 (m) cc_final: 0.8083 (p)
REVERT: C  339 TRP cc_start: 0.8391 (m100) cc_final: 0.7999 (m100)
REVERT: H   86 LEU cc_start: 0.7653 (mt) cc_final: 0.7444 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0949
  time to fit residues: 31.3745
Evaluate side-chains
  204 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    0.0770
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.2234

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
C  32 GLN
C 119 ASN
H 179 GLN
H 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.142297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123255 restraints weight = 13858.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.12
r_work: 0.3520 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8872  Z= 0.128
  Angle     :  0.646   6.390  12107  Z= 0.339
  Chirality :  0.044   0.154   1440
  Planarity :  0.005   0.053   1531
  Dihedral  :  5.375  54.712   1259
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.09 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.24), residues: 1168
  helix:  0.74 (0.26), residues: 413
  sheet: -0.49 (0.29), residues: 266
  loop : -0.80 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 209 
 TYR   0.019   0.002   TYR G  40 
 PHE   0.015   0.001   PHE B 251 
 TRP   0.027   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8866)
  covalent geometry    : angle       0.64520 (12095)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       1.28822 (   12)
  hydrogen bonds       : bond        0.04415 (  444)
  hydrogen bonds       : angle       5.53547 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 231
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 TRP cc_start: 0.7618 (m100) cc_final: 0.7041 (m100)
REVERT: A   93 PHE cc_start: 0.7683 (t80) cc_final: 0.7258 (t80)
REVERT: A  109 CYS cc_start: 0.6306 (t) cc_final: 0.6062 (t)
REVERT: A  120 MET cc_start: 0.7067 (mtt) cc_final: 0.6772 (mtp)
REVERT: A  174 TYR cc_start: 0.7140 (m-80) cc_final: 0.6938 (m-80)
REVERT: A  209 MET cc_start: 0.7533 (mmp) cc_final: 0.7181 (mmt)
REVERT: A  224 THR cc_start: 0.7989 (m) cc_final: 0.7678 (p)
REVERT: A  243 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7792 (mtmm)
REVERT: B   15 ARG cc_start: 0.8510 (ttt90) cc_final: 0.8106 (ttt180)
REVERT: B   32 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7546 (ttmm)
REVERT: B  189 HIS cc_start: 0.7657 (p-80) cc_final: 0.7292 (p-80)
REVERT: B  272 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7923 (ttpt)
REVERT: B  303 TYR cc_start: 0.8457 (t80) cc_final: 0.8070 (t80)
REVERT: B  305 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: B  320 TYR cc_start: 0.8850 (m-80) cc_final: 0.8467 (m-80)
REVERT: B  330 ASN cc_start: 0.7678 (t0) cc_final: 0.7190 (t0)
REVERT: B  346 ASN cc_start: 0.8037 (m-40) cc_final: 0.7822 (m-40)
REVERT: C   35 ASN cc_start: 0.8084 (t0) cc_final: 0.7501 (p0)
REVERT: C   59 TYR cc_start: 0.8176 (m-80) cc_final: 0.7770 (m-80)
REVERT: C  175 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7441 (mm-40)
REVERT: C  227 SER cc_start: 0.8690 (t) cc_final: 0.8329 (m)
REVERT: C  274 THR cc_start: 0.8380 (m) cc_final: 0.8062 (p)
REVERT: C  291 ASP cc_start: 0.7952 (p0) cc_final: 0.7375 (p0)
REVERT: H   38 ARG cc_start: 0.8409 (ptt-90) cc_final: 0.8178 (ptt180)
REVERT: H   86 LEU cc_start: 0.7585 (mt) cc_final: 0.7362 (mt)
REVERT: H  192 MET cc_start: 0.7312 (ptm) cc_final: 0.7032 (ttp)
  outliers start: 15
  outliers final: 9
  residues processed: 237
  average time/residue: 0.0853
  time to fit residues: 27.2204
Evaluate side-chains
  231 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 222
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue   17 LYS
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 78 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0980
   chunk 93 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
B 245 HIS
B 312 ASN
C  88 ASN
C 119 ASN
C 239 ASN
C 266 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 179 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.140508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121528 restraints weight = 13538.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.10
r_work: 0.3493 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8872  Z= 0.165
  Angle     :  0.625   9.621  12107  Z= 0.327
  Chirality :  0.043   0.152   1440
  Planarity :  0.005   0.049   1531
  Dihedral  :  5.076  46.160   1259
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.59 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.25), residues: 1168
  helix:  0.82 (0.26), residues: 420
  sheet: -0.29 (0.29), residues: 265
  loop : -0.74 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 129 
 TYR   0.015   0.002   TYR C 111 
 PHE   0.017   0.002   PHE C 180 
 TRP   0.027   0.002   TRP C  82 
 HIS   0.005   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8866)
  covalent geometry    : angle       0.62460 (12095)
  SS BOND              : bond        0.00249 (    6)
  SS BOND              : angle       1.06136 (   12)
  hydrogen bonds       : bond        0.04206 (  444)
  hydrogen bonds       : angle       5.21991 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 230
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7831 (t80) cc_final: 0.7322 (t80)
REVERT: A  159 VAL cc_start: 0.8097 (t) cc_final: 0.7894 (t)
REVERT: A  174 TYR cc_start: 0.7308 (m-80) cc_final: 0.7069 (m-80)
REVERT: A  209 MET cc_start: 0.7516 (mmp) cc_final: 0.7189 (mmt)
REVERT: A  224 THR cc_start: 0.8030 (m) cc_final: 0.7732 (p)
REVERT: B   15 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8106 (ttt180)
REVERT: B   32 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7730 (ttmm)
REVERT: B  189 HIS cc_start: 0.7695 (p-80) cc_final: 0.7408 (p-80)
REVERT: B  272 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8049 (ttpp)
REVERT: B  303 TYR cc_start: 0.8456 (t80) cc_final: 0.8012 (t80)
REVERT: B  305 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: B  320 TYR cc_start: 0.8919 (m-80) cc_final: 0.8570 (m-80)
REVERT: C   35 ASN cc_start: 0.7928 (t0) cc_final: 0.7443 (p0)
REVERT: C   59 TYR cc_start: 0.8157 (m-80) cc_final: 0.7632 (m-80)
REVERT: C  130 GLU cc_start: 0.7345 (mp0) cc_final: 0.7042 (mp0)
REVERT: C  227 SER cc_start: 0.8660 (t) cc_final: 0.8312 (m)
REVERT: C  251 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7403 (mtt-85)
REVERT: C  274 THR cc_start: 0.8513 (m) cc_final: 0.8218 (p)
REVERT: C  291 ASP cc_start: 0.7905 (p0) cc_final: 0.7470 (p0)
REVERT: H  192 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7168 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 238
  average time/residue: 0.0766
  time to fit residues: 24.7233
Evaluate side-chains
  247 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 226
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  312 ASN
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0020
   chunk 12 optimal weight:    0.0070
   chunk 45 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.3806

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
B 312 ASN
B 347 ASN
C  17 GLN
C  88 ASN
C 119 ASN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
H 179 GLN
H 194 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.141378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.122476 restraints weight = 13785.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.14
r_work: 0.3497 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8872  Z= 0.130
  Angle     :  0.594   9.415  12107  Z= 0.308
  Chirality :  0.042   0.138   1440
  Planarity :  0.005   0.052   1531
  Dihedral  :  4.826  41.519   1259
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.29 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.25), residues: 1168
  helix:  0.99 (0.26), residues: 419
  sheet: -0.36 (0.29), residues: 280
  loop : -0.55 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 129 
 TYR   0.016   0.001   TYR H 190 
 PHE   0.014   0.001   PHE C 151 
 TRP   0.024   0.002   TRP C  82 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8866)
  covalent geometry    : angle       0.59309 (12095)
  SS BOND              : bond        0.00234 (    6)
  SS BOND              : angle       1.33985 (   12)
  hydrogen bonds       : bond        0.03762 (  444)
  hydrogen bonds       : angle       5.04451 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 229
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7828 (t80) cc_final: 0.7333 (t80)
REVERT: A  133 ASP cc_start: 0.6177 (t0) cc_final: 0.5859 (t0)
REVERT: A  159 VAL cc_start: 0.8004 (t) cc_final: 0.7790 (t)
REVERT: A  209 MET cc_start: 0.7537 (mmp) cc_final: 0.7218 (mmt)
REVERT: A  224 THR cc_start: 0.7989 (m) cc_final: 0.7694 (p)
REVERT: B   15 ARG cc_start: 0.8517 (ttt90) cc_final: 0.8092 (ttt180)
REVERT: B   32 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7743 (ttmm)
REVERT: B  189 HIS cc_start: 0.7723 (p-80) cc_final: 0.7446 (p-80)
REVERT: B  272 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8076 (ttpp)
REVERT: B  303 TYR cc_start: 0.8429 (t80) cc_final: 0.8102 (t80)
REVERT: B  305 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8189 (tm-30)
REVERT: B  320 TYR cc_start: 0.8912 (m-80) cc_final: 0.8603 (m-80)
REVERT: B  341 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7898 (m-30)
REVERT: C   32 GLN cc_start: 0.7013 (pt0) cc_final: 0.6516 (pt0)
REVERT: C   35 ASN cc_start: 0.7606 (t0) cc_final: 0.7313 (p0)
REVERT: C   59 TYR cc_start: 0.8070 (m-80) cc_final: 0.7542 (m-80)
REVERT: C  128 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8357 (t)
REVERT: C  130 GLU cc_start: 0.7475 (mp0) cc_final: 0.7077 (mp0)
REVERT: C  227 SER cc_start: 0.8697 (t) cc_final: 0.8371 (m)
REVERT: C  234 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7480 (m-80)
REVERT: C  251 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7591 (mtt-85)
REVERT: C  274 THR cc_start: 0.8486 (m) cc_final: 0.8200 (p)
REVERT: C  291 ASP cc_start: 0.7943 (p0) cc_final: 0.7700 (p0)
REVERT: H   38 ARG cc_start: 0.8428 (ptt-90) cc_final: 0.8188 (ptt180)
  outliers start: 32
  outliers final: 22
  residues processed: 242
  average time/residue: 0.0908
  time to fit residues: 29.7521
Evaluate side-chains
  249 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 224
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  290 GLU
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain F residue   38 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0070
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
B 331 ASN
B 347 ASN
C  88 ASN
H  82 GLN
H 183 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.139720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.120923 restraints weight = 13623.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.10
r_work: 0.3472 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8872  Z= 0.174
  Angle     :  0.614   9.536  12107  Z= 0.319
  Chirality :  0.043   0.161   1440
  Planarity :  0.005   0.054   1531
  Dihedral  :  4.851  37.665   1259
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.45 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1168
  helix:  0.95 (0.26), residues: 419
  sheet: -0.43 (0.29), residues: 287
  loop : -0.54 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 180 
 TYR   0.017   0.002   TYR H 190 
 PHE   0.017   0.002   PHE C 151 
 TRP   0.023   0.002   TRP C  82 
 HIS   0.005   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8866)
  covalent geometry    : angle       0.61355 (12095)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       1.08692 (   12)
  hydrogen bonds       : bond        0.03876 (  444)
  hydrogen bonds       : angle       5.06511 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 221
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7862 (t80) cc_final: 0.7345 (t80)
REVERT: A  133 ASP cc_start: 0.6170 (t0) cc_final: 0.5955 (t0)
REVERT: A  174 TYR cc_start: 0.7786 (m-80) cc_final: 0.7475 (t80)
REVERT: A  209 MET cc_start: 0.7577 (mmp) cc_final: 0.7249 (mmt)
REVERT: A  224 THR cc_start: 0.7986 (m) cc_final: 0.7669 (p)
REVERT: B   15 ARG cc_start: 0.8510 (ttt90) cc_final: 0.8095 (ttt180)
REVERT: B   32 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7730 (ttmm)
REVERT: B  189 HIS cc_start: 0.7786 (p-80) cc_final: 0.7448 (p-80)
REVERT: B  193 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8233 (mtpt)
REVERT: B  272 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8035 (ttpp)
REVERT: B  303 TYR cc_start: 0.8437 (t80) cc_final: 0.8150 (t80)
REVERT: B  305 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: B  320 TYR cc_start: 0.8931 (m-80) cc_final: 0.8671 (m-80)
REVERT: B  341 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7906 (m-30)
REVERT: C   32 GLN cc_start: 0.6928 (pt0) cc_final: 0.6511 (pt0)
REVERT: C   59 TYR cc_start: 0.8105 (m-80) cc_final: 0.7537 (m-80)
REVERT: C  128 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8470 (t)
REVERT: C  129 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6924 (ttp-110)
REVERT: C  130 GLU cc_start: 0.7410 (mp0) cc_final: 0.6773 (mp0)
REVERT: C  227 SER cc_start: 0.8766 (t) cc_final: 0.8453 (m)
REVERT: C  234 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7540 (m-80)
REVERT: C  251 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7583 (mtt-85)
REVERT: C  274 THR cc_start: 0.8521 (m) cc_final: 0.8256 (p)
REVERT: C  291 ASP cc_start: 0.7891 (p0) cc_final: 0.7653 (p0)
REVERT: H  147 VAL cc_start: 0.7936 (p) cc_final: 0.7377 (m)
  outliers start: 35
  outliers final: 24
  residues processed: 236
  average time/residue: 0.0866
  time to fit residues: 27.7511
Evaluate side-chains
  245 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 112 optimal weight:   20.0000
   chunk 113 optimal weight:    0.0170
   chunk 9 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
B 331 ASN
B 347 ASN
C  17 GLN
H  82 GLN
H 179 GLN
H 183 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.140298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.121547 restraints weight = 13660.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.10
r_work: 0.3452 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8872  Z= 0.147
  Angle     :  0.605  10.248  12107  Z= 0.309
  Chirality :  0.042   0.149   1440
  Planarity :  0.005   0.054   1531
  Dihedral  :  4.703  34.478   1259
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.97 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.25), residues: 1168
  helix:  1.06 (0.26), residues: 416
  sheet: -0.44 (0.30), residues: 287
  loop : -0.57 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H 180 
 TYR   0.018   0.002   TYR H 190 
 PHE   0.014   0.001   PHE C 151 
 TRP   0.020   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8866)
  covalent geometry    : angle       0.60399 (12095)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       1.24762 (   12)
  hydrogen bonds       : bond        0.03641 (  444)
  hydrogen bonds       : angle       4.97625 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 222
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7859 (t80) cc_final: 0.7343 (t80)
REVERT: A   97 LEU cc_start: 0.8319 (pp) cc_final: 0.8107 (pp)
REVERT: A  159 VAL cc_start: 0.7877 (t) cc_final: 0.7561 (p)
REVERT: A  174 TYR cc_start: 0.7808 (m-80) cc_final: 0.7427 (t80)
REVERT: A  209 MET cc_start: 0.7618 (mmp) cc_final: 0.7276 (mmt)
REVERT: A  224 THR cc_start: 0.7973 (m) cc_final: 0.7486 (p)
REVERT: B   15 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8038 (ttt180)
REVERT: B   32 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7709 (ttmm)
REVERT: B  189 HIS cc_start: 0.7800 (p-80) cc_final: 0.7580 (p-80)
REVERT: B  193 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8217 (mtpt)
REVERT: B  272 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8046 (ttpp)
REVERT: B  303 TYR cc_start: 0.8424 (t80) cc_final: 0.8079 (t80)
REVERT: B  305 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: B  341 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7891 (m-30)
REVERT: C   59 TYR cc_start: 0.8077 (m-80) cc_final: 0.7532 (m-80)
REVERT: C  128 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8268 (t)
REVERT: C  129 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6978 (ttp-110)
REVERT: C  130 GLU cc_start: 0.7448 (mp0) cc_final: 0.6820 (mp0)
REVERT: C  227 SER cc_start: 0.8764 (t) cc_final: 0.8443 (m)
REVERT: C  234 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7555 (m-80)
REVERT: C  251 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7543 (mtt-85)
REVERT: C  274 THR cc_start: 0.8519 (m) cc_final: 0.8256 (p)
REVERT: C  291 ASP cc_start: 0.7864 (p0) cc_final: 0.7459 (p0)
REVERT: H   38 ARG cc_start: 0.8400 (ptt180) cc_final: 0.8162 (ptt180)
REVERT: H  147 VAL cc_start: 0.7973 (p) cc_final: 0.7340 (m)
  outliers start: 34
  outliers final: 28
  residues processed: 238
  average time/residue: 0.0899
  time to fit residues: 28.8037
Evaluate side-chains
  254 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 223
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  290 GLU
Chi-restraints excluded: chain B residue  312 ASN
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain F residue   47 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
B 333 GLN
B 347 ASN
C  17 GLN
C  32 GLN
H 179 GLN
H 183 GLN
F  67 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.138908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.120159 restraints weight = 13719.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.09
r_work: 0.3455 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8872  Z= 0.214
  Angle     :  0.655  10.313  12107  Z= 0.337
  Chirality :  0.044   0.159   1440
  Planarity :  0.005   0.063   1531
  Dihedral  :  4.877  33.336   1259
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 16.43 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.25), residues: 1168
  helix:  0.83 (0.26), residues: 424
  sheet: -0.42 (0.30), residues: 279
  loop : -0.67 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H 180 
 TYR   0.017   0.002   TYR H 190 
 PHE   0.020   0.002   PHE C 151 
 TRP   0.021   0.002   TRP C  82 
 HIS   0.006   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8866)
  covalent geometry    : angle       0.65376 (12095)
  SS BOND              : bond        0.00303 (    6)
  SS BOND              : angle       1.34910 (   12)
  hydrogen bonds       : bond        0.03972 (  444)
  hydrogen bonds       : angle       5.13532 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 228
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7872 (t80) cc_final: 0.7375 (t80)
REVERT: A  174 TYR cc_start: 0.7816 (m-80) cc_final: 0.7296 (t80)
REVERT: A  199 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7701 (mtpt)
REVERT: A  209 MET cc_start: 0.7615 (mmp) cc_final: 0.7288 (mmt)
REVERT: A  224 THR cc_start: 0.8123 (m) cc_final: 0.7724 (p)
REVERT: B   15 ARG cc_start: 0.8612 (ttt90) cc_final: 0.8151 (ttt180)
REVERT: B   32 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7733 (ttmm)
REVERT: B  189 HIS cc_start: 0.7963 (p-80) cc_final: 0.7487 (p-80)
REVERT: B  193 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8219 (mtpt)
REVERT: B  272 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8095 (ttpp)
REVERT: B  303 TYR cc_start: 0.8432 (t80) cc_final: 0.8148 (t80)
REVERT: B  305 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: B  341 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7914 (m-30)
REVERT: C   59 TYR cc_start: 0.8118 (m-80) cc_final: 0.7562 (m-80)
REVERT: C  128 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8245 (t)
REVERT: C  130 GLU cc_start: 0.7484 (mp0) cc_final: 0.6858 (mp0)
REVERT: C  175 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7432 (mm-40)
REVERT: C  227 SER cc_start: 0.8753 (t) cc_final: 0.8443 (m)
REVERT: C  234 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7562 (m-80)
REVERT: C  251 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7577 (mtt-85)
REVERT: C  274 THR cc_start: 0.8522 (m) cc_final: 0.8268 (p)
REVERT: C  291 ASP cc_start: 0.7905 (p0) cc_final: 0.7640 (p0)
  outliers start: 36
  outliers final: 28
  residues processed: 245
  average time/residue: 0.1051
  time to fit residues: 34.5355
Evaluate side-chains
  254 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 223
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  219 LEU
Chi-restraints excluded: chain F residue   47 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 104 optimal weight:    0.2980
   chunk 111 optimal weight:    6.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
C  17 GLN
C  32 GLN
H 179 GLN
H 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.141153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122487 restraints weight = 13518.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.09
r_work: 0.3487 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8872  Z= 0.125
  Angle     :  0.604  10.686  12107  Z= 0.305
  Chirality :  0.042   0.136   1440
  Planarity :  0.005   0.086   1531
  Dihedral  :  4.604  30.088   1259
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.48 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1168
  helix:  1.09 (0.26), residues: 421
  sheet: -0.44 (0.30), residues: 283
  loop : -0.57 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG H 180 
 TYR   0.017   0.001   TYR H 190 
 PHE   0.012   0.001   PHE C 151 
 TRP   0.018   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8866)
  covalent geometry    : angle       0.60229 (12095)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       1.49052 (   12)
  hydrogen bonds       : bond        0.03463 (  444)
  hydrogen bonds       : angle       4.89844 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 222
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7860 (t80) cc_final: 0.7372 (t80)
REVERT: A  159 VAL cc_start: 0.7775 (t) cc_final: 0.7451 (p)
REVERT: A  174 TYR cc_start: 0.7741 (m-80) cc_final: 0.7443 (t80)
REVERT: A  209 MET cc_start: 0.7591 (mmp) cc_final: 0.7262 (mmt)
REVERT: A  224 THR cc_start: 0.7977 (m) cc_final: 0.7622 (p)
REVERT: B   15 ARG cc_start: 0.8582 (ttt90) cc_final: 0.8097 (ttt180)
REVERT: B   32 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7673 (ttmm)
REVERT: B  189 HIS cc_start: 0.7861 (p-80) cc_final: 0.7635 (p-80)
REVERT: B  193 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8196 (mtpt)
REVERT: B  272 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8070 (ttpp)
REVERT: B  303 TYR cc_start: 0.8372 (t80) cc_final: 0.7980 (t80)
REVERT: B  305 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8074 (tm-30)
REVERT: C   32 GLN cc_start: 0.6907 (pt0) cc_final: 0.6606 (pt0)
REVERT: C   59 TYR cc_start: 0.8009 (m-80) cc_final: 0.7529 (m-80)
REVERT: C  128 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8263 (t)
REVERT: C  130 GLU cc_start: 0.7538 (mp0) cc_final: 0.6968 (mp0)
REVERT: C  175 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7558 (mm-40)
REVERT: C  227 SER cc_start: 0.8736 (t) cc_final: 0.8420 (m)
REVERT: C  234 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7569 (m-80)
REVERT: C  251 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7515 (mtt-85)
REVERT: C  274 THR cc_start: 0.8531 (m) cc_final: 0.8279 (p)
REVERT: C  291 ASP cc_start: 0.7942 (p0) cc_final: 0.7497 (p0)
REVERT: H   95 TYR cc_start: 0.7883 (m-80) cc_final: 0.7407 (m-80)
  outliers start: 33
  outliers final: 28
  residues processed: 238
  average time/residue: 0.1014
  time to fit residues: 32.8000
Evaluate side-chains
  251 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  290 GLU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain F residue   47 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 84 optimal weight:    0.4980
   chunk 60 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
C  17 GLN
H 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.139423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.120843 restraints weight = 13624.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.08
r_work: 0.3482 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8872  Z= 0.181
  Angle     :  0.637  10.857  12107  Z= 0.323
  Chirality :  0.043   0.138   1440
  Planarity :  0.005   0.056   1531
  Dihedral  :  4.699  29.051   1259
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 17.72 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.25), residues: 1168
  helix:  0.99 (0.26), residues: 421
  sheet: -0.52 (0.30), residues: 281
  loop : -0.65 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 129 
 TYR   0.016   0.002   TYR H 190 
 PHE   0.017   0.002   PHE C 180 
 TRP   0.019   0.002   TRP C  82 
 HIS   0.005   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8866)
  covalent geometry    : angle       0.63630 (12095)
  SS BOND              : bond        0.00251 (    6)
  SS BOND              : angle       0.95060 (   12)
  hydrogen bonds       : bond        0.03737 (  444)
  hydrogen bonds       : angle       5.03157 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.6275 (t0) cc_final: 0.6026 (t0)
REVERT: A  159 VAL cc_start: 0.7824 (t) cc_final: 0.7501 (p)
REVERT: A  174 TYR cc_start: 0.7678 (m-80) cc_final: 0.7230 (t80)
REVERT: A  199 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7626 (mtpt)
REVERT: A  209 MET cc_start: 0.7605 (mmp) cc_final: 0.7360 (mmt)
REVERT: A  224 THR cc_start: 0.8083 (m) cc_final: 0.7719 (p)
REVERT: B   15 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8119 (ttt180)
REVERT: B   32 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7681 (ttmm)
REVERT: B  189 HIS cc_start: 0.8011 (p-80) cc_final: 0.7317 (p-80)
REVERT: B  193 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8218 (mtpt)
REVERT: B  272 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8087 (ttpp)
REVERT: B  303 TYR cc_start: 0.8388 (t80) cc_final: 0.8070 (t80)
REVERT: B  305 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: C   59 TYR cc_start: 0.8002 (m-80) cc_final: 0.7517 (m-80)
REVERT: C  128 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8215 (t)
REVERT: C  129 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6853 (ttp-110)
REVERT: C  130 GLU cc_start: 0.7476 (mp0) cc_final: 0.6851 (mp0)
REVERT: C  175 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7569 (mm-40)
REVERT: C  219 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7966 (ttm-80)
REVERT: C  227 SER cc_start: 0.8720 (t) cc_final: 0.8402 (m)
REVERT: C  234 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7640 (m-80)
REVERT: C  251 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7577 (mtt-85)
REVERT: C  274 THR cc_start: 0.8527 (m) cc_final: 0.8269 (p)
REVERT: C  291 ASP cc_start: 0.7917 (p0) cc_final: 0.7480 (p0)
  outliers start: 30
  outliers final: 28
  residues processed: 235
  average time/residue: 0.1094
  time to fit residues: 34.6501
Evaluate side-chains
  250 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  290 GLU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain F residue   47 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:    0.0030
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 74 optimal weight:    0.1980
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
C  17 GLN
C  32 GLN
H 179 GLN
H 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.141060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.122476 restraints weight = 13512.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.08
r_work: 0.3493 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8872  Z= 0.128
  Angle     :  0.608  11.153  12107  Z= 0.307
  Chirality :  0.042   0.144   1440
  Planarity :  0.004   0.055   1531
  Dihedral  :  4.529  26.490   1259
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.83 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.25), residues: 1168
  helix:  1.12 (0.26), residues: 421
  sheet: -0.38 (0.31), residues: 266
  loop : -0.63 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 129 
 TYR   0.016   0.001   TYR H 190 
 PHE   0.012   0.001   PHE C 151 
 TRP   0.019   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8866)
  covalent geometry    : angle       0.60746 (12095)
  SS BOND              : bond        0.00265 (    6)
  SS BOND              : angle       1.16606 (   12)
  hydrogen bonds       : bond        0.03425 (  444)
  hydrogen bonds       : angle       4.89360 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 VAL cc_start: 0.7747 (t) cc_final: 0.7436 (p)
REVERT: A  174 TYR cc_start: 0.7610 (m-80) cc_final: 0.7347 (t80)
REVERT: A  209 MET cc_start: 0.7565 (mmp) cc_final: 0.7314 (mmt)
REVERT: A  224 THR cc_start: 0.7950 (m) cc_final: 0.7622 (p)
REVERT: B   15 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8196 (ttt180)
REVERT: B   32 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7661 (ttmm)
REVERT: B  189 HIS cc_start: 0.7989 (p-80) cc_final: 0.7324 (p-80)
REVERT: B  193 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8193 (mtpt)
REVERT: B  272 LYS cc_start: 0.8272 (ttpp) cc_final: 0.8048 (ttpp)
REVERT: B  303 TYR cc_start: 0.8349 (t80) cc_final: 0.7872 (t80)
REVERT: B  305 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: C   32 GLN cc_start: 0.6901 (pt0) cc_final: 0.6605 (pt0)
REVERT: C   59 TYR cc_start: 0.8057 (m-80) cc_final: 0.7540 (m-10)
REVERT: C  128 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8266 (t)
REVERT: C  130 GLU cc_start: 0.7501 (mp0) cc_final: 0.6944 (mp0)
REVERT: C  175 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7600 (mm-40)
REVERT: C  219 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7933 (ttm-80)
REVERT: C  227 SER cc_start: 0.8685 (t) cc_final: 0.8386 (m)
REVERT: C  234 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7658 (m-80)
REVERT: C  251 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7556 (mtt-85)
REVERT: C  274 THR cc_start: 0.8535 (m) cc_final: 0.8283 (p)
REVERT: C  291 ASP cc_start: 0.7901 (p0) cc_final: 0.7511 (p0)
REVERT: H   95 TYR cc_start: 0.7859 (m-80) cc_final: 0.7440 (m-80)
  outliers start: 29
  outliers final: 26
  residues processed: 233
  average time/residue: 0.1091
  time to fit residues: 34.4940
Evaluate side-chains
  245 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 217
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  290 GLU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain F residue   47 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 78 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0370
   chunk 22 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   overall best weight:    0.3034

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
C  17 GLN
H  82 GLN
H 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.140472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.122207 restraints weight = 13571.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.02
r_work: 0.3514 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8872  Z= 0.118
  Angle     :  0.598  10.949  12107  Z= 0.301
  Chirality :  0.042   0.143   1440
  Planarity :  0.004   0.056   1531
  Dihedral  :  4.389  23.406   1259
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.48 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.25), residues: 1168
  helix:  1.25 (0.26), residues: 416
  sheet: -0.43 (0.31), residues: 271
  loop : -0.59 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 129 
 TYR   0.015   0.001   TYR H 190 
 PHE   0.011   0.001   PHE C 151 
 TRP   0.017   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8866)
  covalent geometry    : angle       0.59613 (12095)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       1.49331 (   12)
  hydrogen bonds       : bond        0.03323 (  444)
  hydrogen bonds       : angle       4.81656 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2710.03 seconds
wall clock time: 47 minutes 2.86 seconds (2822.86 seconds total)