Starting phenix.real_space_refine
on Wed Feb  4 01:35:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9umj_64276/02_2026/9umj_64276.map"
  }
  resolution = 3.38
  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=   0.001 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      53      5.16       5
     C    5221      2.51       5
     N    1396      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 8158
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 50
          Classifications: {'peptide': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 3}
    Chain: "D"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 1}
    Chain: "C"
      Number of atoms: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2147
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 12, 'TRANS': 267}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1554
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 4, 'TRANS': 203}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "B"
      Number of atoms: 2382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2382
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 219
          Unresolved non-hydrogen angles: 272
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 126
    Chain: "G"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 364
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "H"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1644
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 67
  Time building chain proxies: 1.66, per 1000 atoms: 0.20
  Number of scatterers: 8158
  At special positions: 0
  Unit cell: (87.8178, 121.128, 125.67, 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      53     16.00
     O    1488      8.00
     N    1396      7.00
     C    5221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " DAL D   9 " - " LEU D   8 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 316.1 milliseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL D   9 "
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      37.8% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'C' and resid 20 through 51
    Processing helix  chain 'C' and resid 55 through 82
      removed outlier: 4.580A  pdb=" N   TRP C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   PHE C  61 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
      Proline residue:  C  76  - end of helix
    Processing helix  chain 'C' and resid 92 through 126
      Proline residue:  C  99  - end of helix
    Processing helix  chain 'C' and resid 126 through 134
    Processing helix  chain 'C' and resid 135 through 161
      Proline residue:  C 156  - end of helix
    Processing helix  chain 'C' and resid 323 through 357
      removed outlier: 5.231A  pdb=" N   VAL C 340 " --> pdb=" O   VAL C 336 " (cutoff:3.500A)
      Proline residue:  C 341  - end of helix
    Processing helix  chain 'C' and resid 364 through 393
      Proline residue:  C 385  - end of helix
    Processing helix  chain 'C' and resid 400 through 429
      removed outlier: 4.446A  pdb=" N   HIS C 411 " --> pdb=" O   MET C 407 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   MET C 412 " --> pdb=" O   SER C 408 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASN C 420 " --> pdb=" O   LEU C 416 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   SER C 421 " --> pdb=" O   ALA C 417 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   CYS C 422 " --> pdb=" O   SER C 418 " (cutoff:3.500A)
      Proline residue:  C 425  - end of helix
    Processing helix  chain 'C' and resid 432 through 443
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.768A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 216 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 256
      removed outlier: 3.524A  pdb=" N   ASN A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.930A  pdb=" N   ILE A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.517A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.881A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.530A  pdb=" N   ASP H 223 " --> pdb=" O   GLU H 220 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 220 through 224'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 7.176A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.623A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.763A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.791A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.621A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.644A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.777A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.622A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.464A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.944A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 155 through 159
      removed outlier: 3.687A  pdb=" N   ILE H 216 " --> pdb=" O   VAL H 155 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195
      removed outlier: 6.889A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1215 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: 1.30

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2638
        1.34 -     1.46: 1997
        1.46 -     1.58: 3635
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 8340
  Sorted by residual:
  bond pdb=" C   VAL H 149 "
       pdb=" N   THR H 150 "
    ideal  model  delta    sigma   weight residual
    1.329  1.360 -0.031 3.03e-02 1.09e+03 1.04e+00
  bond pdb=" C   SER H 206 "
       pdb=" N   GLY H 207 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.012 1.46e-02 4.69e+03 6.42e-01
  bond pdb=" C   MET C 106 "
       pdb=" O   MET C 106 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.15e-02 7.56e+03 5.99e-01
  bond pdb=" C   GLY H 209 "
       pdb=" N   THR H 210 "
    ideal  model  delta    sigma   weight residual
    1.332  1.322  0.011 1.40e-02 5.10e+03 5.78e-01
  bond pdb=" CG  PRO G  49 "
       pdb=" CD  PRO G  49 "
    ideal  model  delta    sigma   weight residual
    1.503  1.477  0.026 3.40e-02 8.65e+02 5.67e-01
  ... (remaining 8335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 11235
        1.79 -     3.58: 128
        3.58 -     5.38: 17
        5.38 -     7.17: 0
        7.17 -     8.96: 1
  Bond angle restraints: 11381
  Sorted by residual:
  angle pdb=" N   ASN C 360 "
        pdb=" CA  ASN C 360 "
        pdb=" C   ASN C 360 "
      ideal   model   delta    sigma   weight residual
     113.28  109.32    3.96 1.22e+00 6.72e-01 1.05e+01
  angle pdb=" C   VAL H 149 "
        pdb=" N   THR H 150 "
        pdb=" CA  THR H 150 "
      ideal   model   delta    sigma   weight residual
     121.98  130.94   -8.96 3.11e+00 1.03e-01 8.30e+00
  angle pdb=" N   GLY C  91 "
        pdb=" CA  GLY C  91 "
        pdb=" C   GLY C  91 "
      ideal   model   delta    sigma   weight residual
     110.97  114.42   -3.45 1.42e+00 4.96e-01 5.90e+00
  angle pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
        pdb=" CB  MET H 192 "
      ideal   model   delta    sigma   weight residual
     113.65  110.46    3.19 1.47e+00 4.63e-01 4.70e+00
  angle pdb=" N   ARG C 357 "
        pdb=" CA  ARG C 357 "
        pdb=" C   ARG C 357 "
      ideal   model   delta    sigma   weight residual
     112.97  110.67    2.30 1.06e+00 8.90e-01 4.69e+00
  ... (remaining 11376 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 4418
       16.75 -    33.49: 345
       33.49 -    50.24: 58
       50.24 -    66.99: 9
       66.99 -    83.74: 4
  Dihedral angle restraints: 4834
    sinusoidal: 1599
      harmonic: 3235
  Sorted by residual:
  dihedral pdb=" CB  CYS C  95 "
           pdb=" SG  CYS C  95 "
           pdb=" SG  CYS C 172 "
           pdb=" CB  CYS C 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -169.74   83.74     1      1.00e+01 1.00e-02 8.55e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.91   30.91     1      1.00e+01 1.00e-02 1.36e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.61   18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 766
       0.027 -    0.053: 315
       0.053 -    0.080: 162
       0.080 -    0.106: 74
       0.106 -    0.133: 21
  Chirality restraints: 1338
  Sorted by residual:
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1335 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 335 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.21e+00
        pdb=" C   VAL C 335 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   VAL C 335 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL C 336 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER H 184 "    0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO H 185 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO H 185 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO H 185 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 322 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO C 323 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 323 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 323 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1953
        2.79 -     3.32: 7360
        3.32 -     3.84: 13108
        3.84 -     4.37: 14131
        4.37 -     4.90: 26322
  Nonbonded interactions: 62874
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" NH1 ARG B 137 "
            pdb=" O   GLU B 172 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   PHE H  32 "
            pdb=" NH2 ARG H  72 "
     model   vdw
     2.307 3.120
  ... (remaining 62869 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.800
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.790
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
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   0.031   8344  Z= 0.157
  Angle     :  0.512   8.962  11390  Z= 0.282
  Chirality :  0.041   0.133   1338
  Planarity :  0.003   0.033   1447
  Dihedral  : 12.415  82.439   2730
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.63 (0.26), residues: 1095
  helix:  2.21 (0.27), residues: 390
  sheet: -0.18 (0.32), residues: 272
  loop : -0.84 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  87 
 TYR   0.011   0.001   TYR H 101 
 PHE   0.018   0.001   PHE B 235 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8340)
  covalent geometry    : angle       0.51163 (11381)
  SS BOND              : bond        0.00347 (    3)
  SS BOND              : angle       0.43778 (    6)
  hydrogen bonds       : bond        0.17827 (  430)
  hydrogen bonds       : angle       6.85291 ( 1215)
  link_TRANS           : bond        0.00303 (    1)
  link_TRANS           : angle       0.28047 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: C   29 ILE cc_start: 0.7524 (tp) cc_final: 0.7282 (tp)
REVERT: C   47 VAL cc_start: 0.7633 (t) cc_final: 0.7388 (m)
REVERT: C   73 LEU cc_start: 0.7557 (tp) cc_final: 0.7311 (mt)
REVERT: C  117 SER cc_start: 0.7972 (t) cc_final: 0.7716 (m)
REVERT: C  362 THR cc_start: 0.7352 (p) cc_final: 0.7122 (p)
REVERT: C  379 PHE cc_start: 0.7909 (t80) cc_final: 0.7522 (t80)
REVERT: A   17 LYS cc_start: 0.8240 (mtpt) cc_final: 0.8019 (ttmm)
REVERT: A   24 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7344 (mtmt)
REVERT: A   32 LYS cc_start: 0.8033 (mttt) cc_final: 0.7821 (mtpt)
REVERT: A  299 ASP cc_start: 0.6613 (t0) cc_final: 0.6005 (t0)
REVERT: A  305 GLN cc_start: 0.7570 (tt0) cc_final: 0.7331 (tt0)
REVERT: A  308 PHE cc_start: 0.7239 (m-80) cc_final: 0.6844 (m-80)
REVERT: A  311 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7956 (mmmm)
REVERT: A  321 CYS cc_start: 0.7080 (t) cc_final: 0.6812 (t)
REVERT: A  323 MET cc_start: 0.6716 (mmm) cc_final: 0.6202 (tmm)
REVERT: A  341 ASP cc_start: 0.6713 (t0) cc_final: 0.6276 (t0)
REVERT: A  347 ASN cc_start: 0.8106 (m-40) cc_final: 0.7657 (m-40)
REVERT: B   35 ASN cc_start: 0.7556 (t0) cc_final: 0.7039 (p0)
REVERT: B   93 ILE cc_start: 0.7307 (mt) cc_final: 0.7082 (mm)
REVERT: B   99 TRP cc_start: 0.8670 (m100) cc_final: 0.8350 (m100)
REVERT: B  103 CYS cc_start: 0.8102 (p) cc_final: 0.7771 (t)
REVERT: B  239 ASN cc_start: 0.8409 (t0) cc_final: 0.8083 (m-40)
REVERT: B  263 THR cc_start: 0.8365 (p) cc_final: 0.8082 (t)
REVERT: B  317 CYS cc_start: 0.6744 (p) cc_final: 0.6536 (p)
REVERT: B  338 ILE cc_start: 0.8333 (mm) cc_final: 0.8032 (mt)
REVERT: G   42 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6557 (mm-30)
REVERT: H   38 ARG cc_start: 0.8628 (ptt180) cc_final: 0.8383 (ptt180)
REVERT: H   81 LEU cc_start: 0.7954 (tp) cc_final: 0.7745 (tt)
REVERT: H   85 SER cc_start: 0.7847 (t) cc_final: 0.7587 (m)
REVERT: H   90 ASP cc_start: 0.6809 (m-30) cc_final: 0.6465 (m-30)
REVERT: H  142 GLN cc_start: 0.8306 (mt0) cc_final: 0.7934 (mt0)
REVERT: H  193 SER cc_start: 0.7023 (t) cc_final: 0.6603 (p)
REVERT: H  213 THR cc_start: 0.8289 (m) cc_final: 0.7970 (p)
REVERT: H  227 TYR cc_start: 0.8312 (m-80) cc_final: 0.8037 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.0963
  time to fit residues: 33.1876
Evaluate side-chains
  202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
G  18 GLN
H  39 GLN
H 142 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.114005 restraints weight = 12794.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.90
r_work: 0.3281 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8344  Z= 0.243
  Angle     :  0.620   7.367  11390  Z= 0.333
  Chirality :  0.045   0.156   1338
  Planarity :  0.005   0.041   1447
  Dihedral  :  4.352  44.728   1184
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.58 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.42 (0.26), residues: 1095
  helix:  1.90 (0.27), residues: 392
  sheet: -0.08 (0.32), residues: 251
  loop : -0.95 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 180 
 TYR   0.020   0.002   TYR B 105 
 PHE   0.026   0.002   PHE B 235 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.006   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 8340)
  covalent geometry    : angle       0.61922 (11381)
  SS BOND              : bond        0.01110 (    3)
  SS BOND              : angle       1.44286 (    6)
  hydrogen bonds       : bond        0.05285 (  430)
  hydrogen bonds       : angle       5.25666 ( 1215)
  link_TRANS           : bond        0.00410 (    1)
  link_TRANS           : angle       0.39147 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7792 (t) cc_final: 0.7497 (m)
REVERT: C   70 LEU cc_start: 0.7727 (mt) cc_final: 0.7516 (tt)
REVERT: C   73 LEU cc_start: 0.7522 (tp) cc_final: 0.7321 (mt)
REVERT: C  332 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7965 (t)
REVERT: C  436 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7207 (mtt90)
REVERT: A   13 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: A   21 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8429 (ttmm)
REVERT: A   24 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7968 (mtmt)
REVERT: A  198 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8322 (mtp180)
REVERT: A  299 ASP cc_start: 0.6927 (t0) cc_final: 0.6442 (t0)
REVERT: A  308 PHE cc_start: 0.7484 (m-80) cc_final: 0.7118 (m-80)
REVERT: A  311 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8273 (mmmm)
REVERT: A  323 MET cc_start: 0.7577 (mmm) cc_final: 0.6742 (tmm)
REVERT: A  347 ASN cc_start: 0.8305 (m-40) cc_final: 0.7841 (m-40)
REVERT: B   35 ASN cc_start: 0.7859 (t0) cc_final: 0.7399 (p0)
REVERT: B   99 TRP cc_start: 0.8706 (m100) cc_final: 0.8381 (m100)
REVERT: B  263 THR cc_start: 0.8670 (p) cc_final: 0.8375 (t)
REVERT: B  289 TYR cc_start: 0.8655 (m-80) cc_final: 0.8390 (m-80)
REVERT: B  317 CYS cc_start: 0.7940 (p) cc_final: 0.7671 (p)
REVERT: G   42 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: H   38 ARG cc_start: 0.8836 (ptt180) cc_final: 0.8557 (ptt180)
REVERT: H   51 ILE cc_start: 0.8591 (pt) cc_final: 0.8092 (mp)
REVERT: H   90 ASP cc_start: 0.7279 (m-30) cc_final: 0.6886 (m-30)
REVERT: H  193 SER cc_start: 0.7599 (t) cc_final: 0.7189 (p)
  outliers start: 18
  outliers final: 13
  residues processed: 213
  average time/residue: 0.1003
  time to fit residues: 27.9312
Evaluate side-chains
  215 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  332 THR
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
G  18 GLN
H 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.114833 restraints weight = 12749.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.86
r_work: 0.3305 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8344  Z= 0.189
  Angle     :  0.575  11.186  11390  Z= 0.305
  Chirality :  0.043   0.146   1338
  Planarity :  0.004   0.037   1447
  Dihedral  :  4.228  38.474   1184
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.77 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.46 (0.26), residues: 1095
  helix:  2.01 (0.27), residues: 392
  sheet: -0.29 (0.30), residues: 270
  loop : -0.87 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 180 
 TYR   0.013   0.002   TYR H 190 
 PHE   0.019   0.001   PHE B 235 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 8340)
  covalent geometry    : angle       0.57390 (11381)
  SS BOND              : bond        0.00825 (    3)
  SS BOND              : angle       1.56295 (    6)
  hydrogen bonds       : bond        0.04677 (  430)
  hydrogen bonds       : angle       4.95909 ( 1215)
  link_TRANS           : bond        0.00313 (    1)
  link_TRANS           : angle       0.32407 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7753 (t) cc_final: 0.7479 (m)
REVERT: C   75 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7981 (mp)
REVERT: C   77 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7296 (t80)
REVERT: C  126 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8044 (mtpt)
REVERT: C  332 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7881 (t)
REVERT: C  394 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7087 (tt)
REVERT: C  436 ARG cc_start: 0.7556 (mmt90) cc_final: 0.7164 (mtt90)
REVERT: A   13 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8102 (mp)
REVERT: A   17 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8170 (mtmm)
REVERT: A   24 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7925 (mtmt)
REVERT: A  198 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8333 (mtp85)
REVERT: A  225 CYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7533 (p)
REVERT: A  299 ASP cc_start: 0.6831 (t0) cc_final: 0.6336 (t0)
REVERT: A  311 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8273 (mmmm)
REVERT: A  323 MET cc_start: 0.7514 (mmm) cc_final: 0.6781 (tmm)
REVERT: A  342 ILE cc_start: 0.8210 (mt) cc_final: 0.7932 (mm)
REVERT: A  347 ASN cc_start: 0.8292 (m-40) cc_final: 0.7833 (m-40)
REVERT: B   35 ASN cc_start: 0.7861 (t0) cc_final: 0.7311 (p0)
REVERT: B   52 ARG cc_start: 0.7706 (ptp-110) cc_final: 0.7505 (ptp-170)
REVERT: B  221 THR cc_start: 0.8540 (t) cc_final: 0.8233 (p)
REVERT: B  263 THR cc_start: 0.8503 (p) cc_final: 0.8212 (t)
REVERT: B  275 SER cc_start: 0.8569 (p) cc_final: 0.8181 (t)
REVERT: B  289 TYR cc_start: 0.8538 (m-80) cc_final: 0.8319 (m-80)
REVERT: B  317 CYS cc_start: 0.7860 (p) cc_final: 0.7595 (p)
REVERT: G   42 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: H   51 ILE cc_start: 0.8630 (pt) cc_final: 0.8222 (mp)
REVERT: H   90 ASP cc_start: 0.7201 (m-30) cc_final: 0.6947 (m-30)
REVERT: H  193 SER cc_start: 0.7620 (t) cc_final: 0.7217 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 217
  average time/residue: 0.0960
  time to fit residues: 27.4108
Evaluate side-chains
  220 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 198
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  332 THR
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0770
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0570
   chunk 38 optimal weight:    0.0670
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
C 175 ASN
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
G  18 GLN
H 169 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.134521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117172 restraints weight = 12902.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.95
r_work: 0.3343 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8344  Z= 0.108
  Angle     :  0.512  10.487  11390  Z= 0.267
  Chirality :  0.041   0.140   1338
  Planarity :  0.004   0.032   1447
  Dihedral  :  3.886  31.935   1184
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.30 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.61 (0.26), residues: 1095
  helix:  2.17 (0.27), residues: 393
  sheet: -0.34 (0.30), residues: 260
  loop : -0.72 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 180 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.013   0.001   PHE H  80 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.002   0.001   HIS C  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8340)
  covalent geometry    : angle       0.51203 (11381)
  SS BOND              : bond        0.00470 (    3)
  SS BOND              : angle       0.93613 (    6)
  hydrogen bonds       : bond        0.03786 (  430)
  hydrogen bonds       : angle       4.63401 ( 1215)
  link_TRANS           : bond        0.00172 (    1)
  link_TRANS           : angle       0.33052 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7716 (t) cc_final: 0.7452 (m)
REVERT: C   77 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7232 (t80)
REVERT: C  332 THR cc_start: 0.7901 (t) cc_final: 0.7585 (t)
REVERT: C  379 PHE cc_start: 0.7845 (t80) cc_final: 0.7470 (t80)
REVERT: C  394 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6846 (tt)
REVERT: C  436 ARG cc_start: 0.7549 (mmt90) cc_final: 0.7153 (mtt90)
REVERT: A   21 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8409 (ttmm)
REVERT: A   24 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7937 (mtmt)
REVERT: A  299 ASP cc_start: 0.6541 (t0) cc_final: 0.6076 (t0)
REVERT: A  311 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8281 (mmmm)
REVERT: A  323 MET cc_start: 0.7520 (mmm) cc_final: 0.6668 (tmm)
REVERT: A  347 ASN cc_start: 0.8242 (m-40) cc_final: 0.7737 (m-40)
REVERT: B   35 ASN cc_start: 0.7837 (t0) cc_final: 0.7500 (t0)
REVERT: B   52 ARG cc_start: 0.7693 (ptp-110) cc_final: 0.7472 (ptp-170)
REVERT: B  127 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8353 (mptt)
REVERT: B  176 GLN cc_start: 0.8742 (mt0) cc_final: 0.8476 (mt0)
REVERT: B  200 VAL cc_start: 0.8590 (m) cc_final: 0.8324 (p)
REVERT: B  263 THR cc_start: 0.8472 (p) cc_final: 0.8197 (t)
REVERT: B  317 CYS cc_start: 0.7887 (p) cc_final: 0.7566 (p)
REVERT: G   42 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7655 (mm-30)
REVERT: H   51 ILE cc_start: 0.8613 (pt) cc_final: 0.8211 (mp)
REVERT: H   90 ASP cc_start: 0.7174 (m-30) cc_final: 0.6935 (m-30)
REVERT: H  193 SER cc_start: 0.7483 (t) cc_final: 0.7134 (p)
REVERT: H  230 MET cc_start: 0.8538 (ttp) cc_final: 0.8173 (tmm)
  outliers start: 25
  outliers final: 15
  residues processed: 214
  average time/residue: 0.0991
  time to fit residues: 27.5104
Evaluate side-chains
  216 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0970
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 340 ASN
G  18 GLN
H 169 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115934 restraints weight = 12901.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.90
r_work: 0.3319 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8344  Z= 0.150
  Angle     :  0.533   9.787  11390  Z= 0.280
  Chirality :  0.042   0.145   1338
  Planarity :  0.004   0.035   1447
  Dihedral  :  3.970  29.289   1184
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.17 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.59 (0.26), residues: 1095
  helix:  2.15 (0.27), residues: 392
  sheet: -0.27 (0.30), residues: 268
  loop : -0.79 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 198 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.018   0.001   PHE C 369 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8340)
  covalent geometry    : angle       0.53258 (11381)
  SS BOND              : bond        0.00620 (    3)
  SS BOND              : angle       1.26338 (    6)
  hydrogen bonds       : bond        0.04090 (  430)
  hydrogen bonds       : angle       4.62661 ( 1215)
  link_TRANS           : bond        0.00260 (    1)
  link_TRANS           : angle       0.28056 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 203
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7740 (t) cc_final: 0.7286 (m)
REVERT: C   52 MET cc_start: 0.7362 (mmm) cc_final: 0.6599 (mpp)
REVERT: C   77 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7272 (t80)
REVERT: C  332 THR cc_start: 0.7990 (t) cc_final: 0.7684 (t)
REVERT: C  379 PHE cc_start: 0.7890 (t80) cc_final: 0.7552 (t80)
REVERT: C  394 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7099 (tt)
REVERT: C  436 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7174 (mtt90)
REVERT: A   17 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8210 (mtmm)
REVERT: A   21 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8444 (ttmm)
REVERT: A   24 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7838 (mtmt)
REVERT: A  211 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8231 (mmtm)
REVERT: A  299 ASP cc_start: 0.6762 (t0) cc_final: 0.6271 (t0)
REVERT: A  311 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8276 (mmmm)
REVERT: A  323 MET cc_start: 0.7561 (mmm) cc_final: 0.6712 (tmm)
REVERT: A  347 ASN cc_start: 0.8273 (m-40) cc_final: 0.7759 (m-40)
REVERT: B   35 ASN cc_start: 0.7855 (t0) cc_final: 0.7530 (t0)
REVERT: B   99 TRP cc_start: 0.8445 (m100) cc_final: 0.7858 (m100)
REVERT: B  200 VAL cc_start: 0.8599 (m) cc_final: 0.8330 (p)
REVERT: B  219 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7752 (ttm-80)
REVERT: B  263 THR cc_start: 0.8509 (p) cc_final: 0.8230 (t)
REVERT: B  270 ILE cc_start: 0.8871 (pt) cc_final: 0.8471 (mm)
REVERT: B  317 CYS cc_start: 0.7872 (p) cc_final: 0.7558 (p)
REVERT: G   42 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: G   51 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7475 (pt)
REVERT: H   51 ILE cc_start: 0.8661 (pt) cc_final: 0.8218 (mp)
REVERT: H  193 SER cc_start: 0.7549 (t) cc_final: 0.7120 (p)
REVERT: H  230 MET cc_start: 0.8482 (ttp) cc_final: 0.8042 (tmm)
  outliers start: 30
  outliers final: 19
  residues processed: 216
  average time/residue: 0.0972
  time to fit residues: 27.6890
Evaluate side-chains
  214 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.116319 restraints weight = 12698.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.86
r_work: 0.3331 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8344  Z= 0.128
  Angle     :  0.515   9.220  11390  Z= 0.271
  Chirality :  0.042   0.140   1338
  Planarity :  0.004   0.049   1447
  Dihedral  :  3.910  31.011   1184
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 20.46 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.59 (0.26), residues: 1095
  helix:  2.17 (0.27), residues: 392
  sheet: -0.34 (0.30), residues: 271
  loop : -0.75 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 349 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.016   0.001   PHE H  80 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8340)
  covalent geometry    : angle       0.51424 (11381)
  SS BOND              : bond        0.00518 (    3)
  SS BOND              : angle       1.04092 (    6)
  hydrogen bonds       : bond        0.03900 (  430)
  hydrogen bonds       : angle       4.54075 ( 1215)
  link_TRANS           : bond        0.00219 (    1)
  link_TRANS           : angle       0.23868 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7702 (t) cc_final: 0.7259 (m)
REVERT: C   52 MET cc_start: 0.7380 (mmm) cc_final: 0.6621 (mpp)
REVERT: C   77 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7266 (t80)
REVERT: C  332 THR cc_start: 0.7920 (t) cc_final: 0.7610 (t)
REVERT: C  379 PHE cc_start: 0.7880 (t80) cc_final: 0.7552 (t80)
REVERT: C  394 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6974 (tt)
REVERT: C  436 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7164 (mtt90)
REVERT: A   17 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8202 (mtmm)
REVERT: A   21 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8423 (ttmm)
REVERT: A   24 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7813 (mtmt)
REVERT: A  211 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8252 (mmtm)
REVERT: A  299 ASP cc_start: 0.6687 (t0) cc_final: 0.6282 (t0)
REVERT: A  311 LYS cc_start: 0.8499 (mmtm) cc_final: 0.8262 (mmmm)
REVERT: A  323 MET cc_start: 0.7499 (mmm) cc_final: 0.6699 (tmm)
REVERT: A  347 ASN cc_start: 0.8252 (m-40) cc_final: 0.7760 (m-40)
REVERT: B   35 ASN cc_start: 0.8010 (t0) cc_final: 0.7670 (t0)
REVERT: B  127 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8367 (mptt)
REVERT: B  176 GLN cc_start: 0.8745 (mt0) cc_final: 0.8493 (mt0)
REVERT: B  200 VAL cc_start: 0.8601 (m) cc_final: 0.8322 (p)
REVERT: B  219 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7734 (ttm-80)
REVERT: B  263 THR cc_start: 0.8476 (p) cc_final: 0.8231 (t)
REVERT: B  270 ILE cc_start: 0.8875 (pt) cc_final: 0.8492 (mm)
REVERT: B  317 CYS cc_start: 0.7887 (p) cc_final: 0.7575 (p)
REVERT: G   42 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7673 (mm-30)
REVERT: G   51 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7445 (pt)
REVERT: H   51 ILE cc_start: 0.8642 (pt) cc_final: 0.8211 (mp)
REVERT: H  193 SER cc_start: 0.7464 (t) cc_final: 0.7112 (p)
  outliers start: 28
  outliers final: 21
  residues processed: 216
  average time/residue: 0.0961
  time to fit residues: 27.4433
Evaluate side-chains
  223 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 82 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 340 ASN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.115099 restraints weight = 13010.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.89
r_work: 0.3323 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8344  Z= 0.163
  Angle     :  0.542   9.349  11390  Z= 0.286
  Chirality :  0.042   0.143   1338
  Planarity :  0.004   0.054   1447
  Dihedral  :  4.025  34.375   1184
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.33 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.52 (0.26), residues: 1095
  helix:  2.11 (0.27), residues: 392
  sheet: -0.34 (0.30), residues: 271
  loop : -0.81 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 349 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.021   0.002   PHE B 241 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8340)
  covalent geometry    : angle       0.54091 (11381)
  SS BOND              : bond        0.00637 (    3)
  SS BOND              : angle       1.28641 (    6)
  hydrogen bonds       : bond        0.04178 (  430)
  hydrogen bonds       : angle       4.57071 ( 1215)
  link_TRANS           : bond        0.00268 (    1)
  link_TRANS           : angle       0.26281 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 202
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7707 (t) cc_final: 0.7261 (m)
REVERT: C   52 MET cc_start: 0.7470 (mmm) cc_final: 0.6926 (mpp)
REVERT: C   77 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7295 (t80)
REVERT: C  332 THR cc_start: 0.7985 (t) cc_final: 0.7665 (t)
REVERT: C  379 PHE cc_start: 0.7872 (t80) cc_final: 0.7575 (t80)
REVERT: C  394 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7069 (tt)
REVERT: A   21 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8444 (ttmm)
REVERT: A   24 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7846 (mtmt)
REVERT: A   32 LYS cc_start: 0.8225 (mttt) cc_final: 0.8012 (mttt)
REVERT: A  299 ASP cc_start: 0.6743 (t0) cc_final: 0.6244 (t0)
REVERT: A  311 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8283 (mmmm)
REVERT: A  323 MET cc_start: 0.7516 (mmm) cc_final: 0.6735 (tmm)
REVERT: A  347 ASN cc_start: 0.8285 (m-40) cc_final: 0.7784 (m-40)
REVERT: B   35 ASN cc_start: 0.7860 (t0) cc_final: 0.7520 (t0)
REVERT: B  127 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8335 (mptt)
REVERT: B  200 VAL cc_start: 0.8601 (m) cc_final: 0.8324 (p)
REVERT: B  219 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7679 (ttm-80)
REVERT: B  263 THR cc_start: 0.8493 (p) cc_final: 0.8251 (t)
REVERT: B  270 ILE cc_start: 0.8892 (pt) cc_final: 0.8394 (mm)
REVERT: B  275 SER cc_start: 0.8576 (p) cc_final: 0.8193 (t)
REVERT: B  317 CYS cc_start: 0.7900 (p) cc_final: 0.7626 (p)
REVERT: B  320 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (t)
REVERT: G   42 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: G   51 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7471 (pt)
REVERT: G   61 PHE cc_start: 0.7371 (m-80) cc_final: 0.6942 (m-80)
REVERT: H   51 ILE cc_start: 0.8642 (pt) cc_final: 0.8211 (mp)
REVERT: H  193 SER cc_start: 0.7567 (t) cc_final: 0.7182 (p)
REVERT: H  230 MET cc_start: 0.8507 (ttp) cc_final: 0.8196 (tmm)
  outliers start: 32
  outliers final: 24
  residues processed: 215
  average time/residue: 0.0902
  time to fit residues: 25.7846
Evaluate side-chains
  225 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0070
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 99 optimal weight:    0.3980
   chunk 109 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
C  81 HIS
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115953 restraints weight = 12760.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.92
r_work: 0.3321 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8344  Z= 0.143
  Angle     :  0.547  16.239  11390  Z= 0.283
  Chirality :  0.042   0.147   1338
  Planarity :  0.004   0.056   1447
  Dihedral  :  3.991  34.894   1184
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.09 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.55 (0.26), residues: 1095
  helix:  2.12 (0.27), residues: 392
  sheet: -0.28 (0.30), residues: 268
  loop : -0.80 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 349 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.017   0.001   PHE H  80 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8340)
  covalent geometry    : angle       0.54673 (11381)
  SS BOND              : bond        0.00574 (    3)
  SS BOND              : angle       1.14398 (    6)
  hydrogen bonds       : bond        0.04037 (  430)
  hydrogen bonds       : angle       4.52017 ( 1215)
  link_TRANS           : bond        0.00238 (    1)
  link_TRANS           : angle       0.25347 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 VAL cc_start: 0.7702 (t) cc_final: 0.7253 (m)
REVERT: C   52 MET cc_start: 0.7454 (mmm) cc_final: 0.7027 (mpp)
REVERT: C   77 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7248 (t80)
REVERT: C  332 THR cc_start: 0.7938 (t) cc_final: 0.7618 (t)
REVERT: C  379 PHE cc_start: 0.7871 (t80) cc_final: 0.7579 (t80)
REVERT: C  394 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7019 (tt)
REVERT: A   21 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8446 (ttmm)
REVERT: A   24 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7843 (mtmt)
REVERT: A   32 LYS cc_start: 0.8278 (mttt) cc_final: 0.8041 (mttt)
REVERT: A  299 ASP cc_start: 0.6728 (t0) cc_final: 0.6288 (t0)
REVERT: A  311 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8280 (mmmm)
REVERT: A  323 MET cc_start: 0.7520 (mmm) cc_final: 0.6713 (tmm)
REVERT: A  341 ASP cc_start: 0.7225 (t0) cc_final: 0.6947 (t0)
REVERT: A  342 ILE cc_start: 0.8172 (mm) cc_final: 0.7819 (mt)
REVERT: A  347 ASN cc_start: 0.8279 (m-40) cc_final: 0.8018 (m-40)
REVERT: B   35 ASN cc_start: 0.8032 (t0) cc_final: 0.7686 (t0)
REVERT: B   49 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7855 (mmt-90)
REVERT: B  127 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8329 (mptt)
REVERT: B  200 VAL cc_start: 0.8610 (m) cc_final: 0.8330 (p)
REVERT: B  219 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7695 (ttm-80)
REVERT: B  270 ILE cc_start: 0.8881 (pt) cc_final: 0.8407 (mm)
REVERT: B  275 SER cc_start: 0.8626 (p) cc_final: 0.8209 (t)
REVERT: B  317 CYS cc_start: 0.7899 (p) cc_final: 0.7619 (p)
REVERT: G   42 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: G   51 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7455 (pt)
REVERT: G   61 PHE cc_start: 0.7351 (m-80) cc_final: 0.6821 (m-80)
REVERT: H   51 ILE cc_start: 0.8629 (pt) cc_final: 0.8210 (mp)
REVERT: H  193 SER cc_start: 0.7552 (t) cc_final: 0.7174 (p)
REVERT: H  230 MET cc_start: 0.8510 (ttp) cc_final: 0.8163 (tmm)
  outliers start: 27
  outliers final: 21
  residues processed: 219
  average time/residue: 0.0851
  time to fit residues: 24.9318
Evaluate side-chains
  225 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 201
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0970
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
G  18 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 = 0.3674 r_free = 0.3674 target = 0.133990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.116830 restraints weight = 12821.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.92
r_work: 0.3322 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8344  Z= 0.126
  Angle     :  0.541  15.785  11390  Z= 0.279
  Chirality :  0.042   0.153   1338
  Planarity :  0.004   0.059   1447
  Dihedral  :  3.918  34.499   1184
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.98 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.61 (0.26), residues: 1095
  helix:  2.18 (0.28), residues: 392
  sheet: -0.33 (0.30), residues: 273
  loop : -0.72 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 349 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.017   0.001   PHE C 111 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8340)
  covalent geometry    : angle       0.54089 (11381)
  SS BOND              : bond        0.00513 (    3)
  SS BOND              : angle       1.05686 (    6)
  hydrogen bonds       : bond        0.03850 (  430)
  hydrogen bonds       : angle       4.47779 ( 1215)
  link_TRANS           : bond        0.00203 (    1)
  link_TRANS           : angle       0.23684 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: C   52 MET cc_start: 0.7387 (mmm) cc_final: 0.7008 (mpp)
REVERT: C   77 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7256 (t80)
REVERT: C  332 THR cc_start: 0.7864 (t) cc_final: 0.7544 (t)
REVERT: C  379 PHE cc_start: 0.7854 (t80) cc_final: 0.7573 (t80)
REVERT: C  394 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6977 (tt)
REVERT: A   21 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8443 (ttmm)
REVERT: A   24 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7822 (mtmt)
REVERT: A  299 ASP cc_start: 0.6617 (t0) cc_final: 0.6205 (t0)
REVERT: A  311 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8273 (mmmm)
REVERT: A  323 MET cc_start: 0.7505 (mmm) cc_final: 0.6691 (tmm)
REVERT: A  341 ASP cc_start: 0.7248 (t0) cc_final: 0.6935 (t0)
REVERT: A  347 ASN cc_start: 0.8246 (m-40) cc_final: 0.8025 (m-40)
REVERT: B   35 ASN cc_start: 0.8019 (t0) cc_final: 0.7685 (t0)
REVERT: B  127 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8318 (mptt)
REVERT: B  200 VAL cc_start: 0.8606 (m) cc_final: 0.8328 (p)
REVERT: B  219 ARG cc_start: 0.8364 (ttm170) cc_final: 0.7695 (ttm-80)
REVERT: B  270 ILE cc_start: 0.8878 (pt) cc_final: 0.8417 (mm)
REVERT: B  275 SER cc_start: 0.8615 (p) cc_final: 0.8209 (t)
REVERT: B  317 CYS cc_start: 0.7900 (p) cc_final: 0.7600 (p)
REVERT: G   42 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: G   51 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7428 (pt)
REVERT: G   61 PHE cc_start: 0.7354 (m-80) cc_final: 0.6907 (m-80)
REVERT: H   51 ILE cc_start: 0.8614 (pt) cc_final: 0.8174 (mp)
REVERT: H   78 THR cc_start: 0.8425 (m) cc_final: 0.8138 (p)
REVERT: H  193 SER cc_start: 0.7545 (t) cc_final: 0.7117 (p)
REVERT: H  230 MET cc_start: 0.8528 (ttp) cc_final: 0.8168 (tmm)
  outliers start: 26
  outliers final: 20
  residues processed: 215
  average time/residue: 0.0905
  time to fit residues: 25.6644
Evaluate side-chains
  222 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0270
   chunk 23 optimal weight:    0.0970
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 239 ASN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.117747 restraints weight = 12740.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.89
r_work: 0.3331 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8344  Z= 0.117
  Angle     :  0.533  15.622  11390  Z= 0.276
  Chirality :  0.042   0.143   1338
  Planarity :  0.004   0.061   1447
  Dihedral  :  3.854  33.686   1184
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.62 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.63 (0.26), residues: 1095
  helix:  2.18 (0.27), residues: 393
  sheet: -0.35 (0.30), residues: 271
  loop : -0.67 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 349 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.010   0.001   PHE B 235 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8340)
  covalent geometry    : angle       0.53278 (11381)
  SS BOND              : bond        0.00449 (    3)
  SS BOND              : angle       0.94057 (    6)
  hydrogen bonds       : bond        0.03694 (  430)
  hydrogen bonds       : angle       4.44790 ( 1215)
  link_TRANS           : bond        0.00161 (    1)
  link_TRANS           : angle       0.22113 (    3)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: C   52 MET cc_start: 0.7403 (mmm) cc_final: 0.7128 (mpp)
REVERT: C   77 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7216 (t80)
REVERT: C  117 SER cc_start: 0.8381 (t) cc_final: 0.8142 (m)
REVERT: C  332 THR cc_start: 0.7829 (t) cc_final: 0.7484 (t)
REVERT: C  379 PHE cc_start: 0.7864 (t80) cc_final: 0.7630 (t80)
REVERT: C  394 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6906 (tt)
REVERT: A   21 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8484 (ttmm)
REVERT: A   24 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7889 (mtmt)
REVERT: A  299 ASP cc_start: 0.6537 (t0) cc_final: 0.6160 (t0)
REVERT: A  311 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8277 (mmmm)
REVERT: A  323 MET cc_start: 0.7471 (mmm) cc_final: 0.6722 (tmm)
REVERT: A  347 ASN cc_start: 0.8277 (m-40) cc_final: 0.7805 (m-40)
REVERT: B   35 ASN cc_start: 0.7983 (t0) cc_final: 0.7653 (t0)
REVERT: B  127 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8301 (mptt)
REVERT: B  176 GLN cc_start: 0.8773 (mt0) cc_final: 0.8549 (mt0)
REVERT: B  200 VAL cc_start: 0.8620 (m) cc_final: 0.8339 (p)
REVERT: B  219 ARG cc_start: 0.8377 (ttm170) cc_final: 0.7738 (ttm-80)
REVERT: B  251 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8617 (mtp85)
REVERT: B  263 THR cc_start: 0.8450 (p) cc_final: 0.8156 (t)
REVERT: B  270 ILE cc_start: 0.8867 (pt) cc_final: 0.8421 (mm)
REVERT: B  275 SER cc_start: 0.8613 (p) cc_final: 0.8216 (t)
REVERT: B  317 CYS cc_start: 0.7896 (p) cc_final: 0.7571 (p)
REVERT: G   42 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7742 (mm-30)
REVERT: G   61 PHE cc_start: 0.7434 (m-80) cc_final: 0.6945 (m-80)
REVERT: H   51 ILE cc_start: 0.8615 (pt) cc_final: 0.8210 (mp)
REVERT: H  193 SER cc_start: 0.7497 (t) cc_final: 0.7166 (p)
REVERT: H  230 MET cc_start: 0.8487 (ttp) cc_final: 0.8110 (tmm)
  outliers start: 22
  outliers final: 19
  residues processed: 219
  average time/residue: 0.0932
  time to fit residues: 26.6596
Evaluate side-chains
  225 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   77 PHE
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  327 MET
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  394 LEU
Chi-restraints excluded: chain C residue  423 PHE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 74 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 96 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.134495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.117517 restraints weight = 12712.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.89
r_work: 0.3344 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8344  Z= 0.126
  Angle     :  0.548  15.365  11390  Z= 0.283
  Chirality :  0.042   0.140   1338
  Planarity :  0.004   0.064   1447
  Dihedral  :  3.864  33.222   1184
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.74 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.60 (0.26), residues: 1095
  helix:  2.17 (0.27), residues: 393
  sheet: -0.36 (0.30), residues: 270
  loop : -0.71 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 349 
 TYR   0.013   0.001   TYR H  60 
 PHE   0.016   0.001   PHE B 241 
 TRP   0.022   0.001   TRP C 409 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8340)
  covalent geometry    : angle       0.54793 (11381)
  SS BOND              : bond        0.00465 (    3)
  SS BOND              : angle       1.01510 (    6)
  hydrogen bonds       : bond        0.03747 (  430)
  hydrogen bonds       : angle       4.45010 ( 1215)
  link_TRANS           : bond        0.00182 (    1)
  link_TRANS           : angle       0.21455 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1867.94 seconds
wall clock time: 32 minutes 45.04 seconds (1965.04 seconds total)