Starting phenix.real_space_refine
on Fri Aug 22 23:05:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9a_35263/08_2025/8i9a_35263.map"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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      51      5.16       5
     C    5353      2.51       5
     N    1458      2.21       5
     O    1547      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8409
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1858
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2415
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 231
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 103
    Chain: "G"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 400
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "H"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1658
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 140
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 53
    Chain: "C"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2006
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 14, 'TRANS': 257}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 176
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 75
    Chain: "D"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    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}
  Time building chain proxies: 1.78, per 1000 atoms: 0.21
  Number of scatterers: 8409
  At special positions: 0
  Unit cell: (84.64, 119.6, 122.36, 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      51     16.00
     O    1547      8.00
     N    1458      7.00
     C    5353      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    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=2.03
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " DAL D   9 " - " LEU D   8 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 401.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 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:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      39.0% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.539A  pdb=" N   ALA A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 265 through 279
      removed outlier: 3.516A  pdb=" N   ASN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 4.141A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.595A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.792A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.534A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 220 through 224
    Processing helix  chain 'C' and resid 20 through 50
      Proline residue:  C  39  - end of helix
      removed outlier: 3.545A  pdb=" N   VAL C  44 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 74
      removed outlier: 3.519A  pdb=" N   TRP C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE C  61 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 85
      removed outlier: 4.201A  pdb=" N   SER C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 126
      Proline residue:  C  99  - end of helix
      removed outlier: 3.687A  pdb=" N   ASN C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
    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 332 through 345
    Processing helix  chain 'C' and resid 345 through 363
      removed outlier: 3.550A  pdb=" N   VAL C 360 " --> pdb=" O   TYR C 356 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 403
      Proline residue:  C 392  - end of helix
      removed outlier: 3.659A  pdb=" N   LEU C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 435
      removed outlier: 3.924A  pdb=" N   HIS C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   VAL C 419 " --> pdb=" O   SER C 415 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   SER C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   CYS C 429 " --> pdb=" O   SER C 425 " (cutoff:3.500A)
      Proline residue:  C 432  - end of helix
    Processing helix  chain 'C' and resid 439 through 450
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.822A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.755A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.531A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.949A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.674A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.679A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.624A  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: 3.737A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.924A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (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 11 through 12
      removed outlier: 7.005A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.670A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.877A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149
      removed outlier: 6.131A  pdb=" N   VAL H 147 " --> pdb=" O   GLU H 246 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163

    460 hydrogen bonds defined for protein.
    1284 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: 1.35

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1559
        1.33 -     1.45: 2235
        1.45 -     1.57: 4728
        1.57 -     1.69: 0
        1.69 -     1.82: 68
  Bond restraints: 8590
  Sorted by residual:
  bond pdb=" C   PRO G  60 "
       pdb=" O   PRO G  60 "
    ideal  model  delta    sigma   weight residual
    1.239  1.204  0.035 1.22e-02 6.72e+03 8.11e+00
  bond pdb=" N   ARG A 231 "
       pdb=" CA  ARG A 231 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.035 1.30e-02 5.92e+03 7.11e+00
  bond pdb=" N   VAL C 388 "
       pdb=" CA  VAL C 388 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.029 1.17e-02 7.31e+03 6.31e+00
  bond pdb=" N   GLU A 330 "
       pdb=" CA  GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.25e-02 6.40e+03 5.81e+00
  bond pdb=" CA  PHE A 208 "
       pdb=" CB  PHE A 208 "
    ideal  model  delta    sigma   weight residual
    1.526  1.565 -0.039 1.68e-02 3.54e+03 5.34e+00
  ... (remaining 8585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 11132
        1.60 -     3.20: 471
        3.20 -     4.80: 77
        4.80 -     6.40: 13
        6.40 -     8.00: 1
  Bond angle restraints: 11694
  Sorted by residual:
  angle pdb=" C   PHE A 273 "
        pdb=" N   LYS A 274 "
        pdb=" CA  LYS A 274 "
      ideal   model   delta    sigma   weight residual
     120.44  115.14    5.30 1.30e+00 5.92e-01 1.66e+01
  angle pdb=" N   ASP A 272 "
        pdb=" CA  ASP A 272 "
        pdb=" C   ASP A 272 "
      ideal   model   delta    sigma   weight residual
     111.07  107.05    4.02 1.07e+00 8.73e-01 1.41e+01
  angle pdb=" N   LYS A 274 "
        pdb=" CA  LYS A 274 "
        pdb=" C   LYS A 274 "
      ideal   model   delta    sigma   weight residual
     111.07  107.10    3.97 1.07e+00 8.73e-01 1.37e+01
  angle pdb=" N   GLU A  21 "
        pdb=" CA  GLU A  21 "
        pdb=" C   GLU A  21 "
      ideal   model   delta    sigma   weight residual
     111.07  107.25    3.82 1.07e+00 8.73e-01 1.27e+01
  angle pdb=" N   PRO C 156 "
        pdb=" CA  PRO C 156 "
        pdb=" C   PRO C 156 "
      ideal   model   delta    sigma   weight residual
     113.78  108.15    5.63 1.62e+00 3.81e-01 1.21e+01
  ... (remaining 11689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4599
       17.97 -    35.94: 353
       35.94 -    53.90: 62
       53.90 -    71.87: 20
       71.87 -    89.84: 6
  Dihedral angle restraints: 5040
    sinusoidal: 1775
      harmonic: 3265
  Sorted by residual:
  dihedral pdb=" CA  ASN A 279 "
           pdb=" C   ASN A 279 "
           pdb=" N   ARG A 280 "
           pdb=" CA  ARG A 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.35  -27.65     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  PRO G  53 "
           pdb=" C   PRO G  53 "
           pdb=" N   VAL G  54 "
           pdb=" CA  VAL G  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.45  -21.55     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.39   19.61     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 5037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1188
       0.071 -    0.142: 155
       0.142 -    0.213: 6
       0.213 -    0.284: 0
       0.284 -    0.355: 1
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  ASN B 313 "
            pdb=" N   ASN B 313 "
            pdb=" C   ASN B 313 "
            pdb=" CB  ASN B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.15e+00
  chirality pdb=" CB  VAL C 388 "
            pdb=" CA  VAL C 388 "
            pdb=" CG1 VAL C 388 "
            pdb=" CG2 VAL C 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ARG A 333 "
            pdb=" N   ARG A 333 "
            pdb=" C   ARG A 333 "
            pdb=" CB  ARG A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1347 not shown)

  Planarity restraints: 1495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 325 "    0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 326 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 340 "    0.010 2.00e-02 2.50e+03   1.21e-02 2.56e+00
        pdb=" CG  PHE A 340 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 340 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 340 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 340 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 340 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 347 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO C 348 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 348 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 348 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1492 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 41
        2.55 -     3.14: 7128
        3.14 -     3.72: 13063
        3.72 -     4.31: 18059
        4.31 -     4.90: 30403
  Nonbonded interactions: 68694
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     1.959 3.040
  nonbonded pdb=" N   GLU G  47 "
            pdb=" OE1 GLU G  47 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   MET C 138 "
            pdb=" OG  SER C 141 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NH1 ARG C 340 "
            pdb=" OXT ARG D  10 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.302 3.040
  ... (remaining 68689 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.890
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.030
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8594  Z= 0.205
  Angle     :  0.759   8.005  11703  Z= 0.443
  Chirality :  0.046   0.355   1350
  Planarity :  0.005   0.052   1494
  Dihedral  : 14.157  89.840   2916
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.53 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole: -0.11 (0.26), residues: 1103
  helix:  0.57 (0.25), residues: 390
  sheet: -0.38 (0.30), residues: 293
  loop : -0.24 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  68 
 TYR   0.016   0.002   TYR C 393 
 PHE   0.028   0.002   PHE A 340 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.006   0.002   HIS H 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8590)
  covalent geometry    : angle       0.75845 (11694)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.76610 (    6)
  hydrogen bonds       : bond        0.14764 (  455)
  hydrogen bonds       : angle       7.33684 ( 1284)
  link_TRANS           : bond        0.00209 (    1)
  link_TRANS           : angle       0.91325 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 205
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.6924 (mmm) cc_final: 0.6705 (mpp)
REVERT: A  274 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (mttp)
REVERT: A  391 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5514 (m-80)
REVERT: B   67 SER cc_start: 0.8448 (t) cc_final: 0.7878 (t)
REVERT: H  184 SER cc_start: 0.9289 (p) cc_final: 0.8988 (m)
REVERT: D    6 MET cc_start: 0.8072 (tpp) cc_final: 0.7682 (tpp)
  outliers start: 10
  outliers final: 2
  residues processed: 212
  average time/residue: 0.1063
  time to fit residues: 29.8031
Evaluate side-chains
  177 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 173
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  434 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.189230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.144683 restraints weight = 10919.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.144531 restraints weight = 6643.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146488 restraints weight = 4976.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.148961 restraints weight = 3971.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.149020 restraints weight = 3377.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8594  Z= 0.155
  Angle     :  0.642   7.802  11703  Z= 0.341
  Chirality :  0.044   0.171   1350
  Planarity :  0.004   0.053   1494
  Dihedral  :  5.949  54.648   1216
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.01 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1103
  helix:  1.48 (0.26), residues: 395
  sheet: -0.24 (0.30), residues: 288
  loop : -0.03 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  10 
 TYR   0.016   0.002   TYR A 318 
 PHE   0.024   0.002   PHE A 208 
 TRP   0.017   0.002   TRP C  88 
 HIS   0.006   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8590)
  covalent geometry    : angle       0.64119 (11694)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       1.20303 (    6)
  hydrogen bonds       : bond        0.04524 (  455)
  hydrogen bonds       : angle       5.55831 ( 1284)
  link_TRANS           : bond        0.00269 (    1)
  link_TRANS           : angle       1.18849 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 PHE cc_start: 0.8063 (p90) cc_final: 0.7804 (p90)
REVERT: A  309 GLU cc_start: 0.8784 (pm20) cc_final: 0.8455 (pm20)
REVERT: A  330 GLU cc_start: 0.8010 (tp30) cc_final: 0.7553 (tp30)
REVERT: B  234 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: H  184 SER cc_start: 0.9360 (p) cc_final: 0.9061 (m)
REVERT: C   34 PHE cc_start: 0.8668 (t80) cc_final: 0.8153 (t80)
REVERT: C   92 ARG cc_start: 0.7118 (tpt-90) cc_final: 0.5915 (tmm-80)
REVERT: C  160 TYR cc_start: 0.6743 (t80) cc_final: 0.6393 (t80)
REVERT: C  414 MET cc_start: 0.7863 (ppp) cc_final: 0.7615 (ppp)
REVERT: C  418 HIS cc_start: 0.7667 (m90) cc_final: 0.7432 (m90)
  outliers start: 15
  outliers final: 9
  residues processed: 209
  average time/residue: 0.0975
  time to fit residues: 27.3785
Evaluate side-chains
  190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 180
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  210 THR
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  174 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 167 HIS
H 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.188124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.144194 restraints weight = 10681.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144347 restraints weight = 5868.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146135 restraints weight = 4866.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.147896 restraints weight = 3752.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.148225 restraints weight = 3275.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8594  Z= 0.162
  Angle     :  0.623   7.367  11703  Z= 0.326
  Chirality :  0.044   0.156   1350
  Planarity :  0.004   0.048   1494
  Dihedral  :  5.189  58.697   1210
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.87 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1103
  helix:  1.56 (0.26), residues: 405
  sheet: -0.32 (0.30), residues: 277
  loop : -0.00 (0.33), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 160 
 TYR   0.015   0.002   TYR A 318 
 PHE   0.021   0.002   PHE H 212 
 TRP   0.017   0.002   TRP C  88 
 HIS   0.007   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8590)
  covalent geometry    : angle       0.62216 (11694)
  SS BOND              : bond        0.00809 (    3)
  SS BOND              : angle       0.91118 (    6)
  hydrogen bonds       : bond        0.03910 (  455)
  hydrogen bonds       : angle       5.27997 ( 1284)
  link_TRANS           : bond        0.00213 (    1)
  link_TRANS           : angle       1.11210 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 PHE cc_start: 0.8205 (t80) cc_final: 0.8000 (t80)
REVERT: A  280 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7797 (ttp-170)
REVERT: A  309 GLU cc_start: 0.8736 (pm20) cc_final: 0.8468 (pm20)
REVERT: B  168 LEU cc_start: 0.8843 (tp) cc_final: 0.8400 (tt)
REVERT: B  234 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7697 (m-80)
REVERT: H  140 MET cc_start: 0.7961 (mmm) cc_final: 0.7700 (mmm)
REVERT: H  184 SER cc_start: 0.9434 (p) cc_final: 0.9109 (m)
REVERT: C   92 ARG cc_start: 0.7070 (tpt-90) cc_final: 0.5861 (tmm-80)
REVERT: C  107 PHE cc_start: 0.6260 (m-80) cc_final: 0.5939 (m-80)
REVERT: C  355 CYS cc_start: 0.8489 (m) cc_final: 0.8059 (m)
REVERT: C  418 HIS cc_start: 0.7606 (m90) cc_final: 0.7369 (m90)
  outliers start: 23
  outliers final: 16
  residues processed: 199
  average time/residue: 0.1129
  time to fit residues: 29.8389
Evaluate side-chains
  186 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   72 CYS
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  174 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 97 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
H 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.188454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.145878 restraints weight = 11113.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.143967 restraints weight = 7003.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145465 restraints weight = 5564.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.146664 restraints weight = 4741.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147151 restraints weight = 4099.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8594  Z= 0.154
  Angle     :  0.612   8.300  11703  Z= 0.317
  Chirality :  0.044   0.340   1350
  Planarity :  0.004   0.050   1494
  Dihedral  :  5.049  59.784   1210
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.71 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1103
  helix:  1.73 (0.26), residues: 405
  sheet: -0.36 (0.30), residues: 276
  loop :  0.01 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  18 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.023   0.002   PHE A 340 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.007   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8590)
  covalent geometry    : angle       0.61128 (11694)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       0.88303 (    6)
  hydrogen bonds       : bond        0.03651 (  455)
  hydrogen bonds       : angle       5.16972 ( 1284)
  link_TRANS           : bond        0.00201 (    1)
  link_TRANS           : angle       0.96012 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 192
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  280 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7768 (ttp-170)
REVERT: A  309 GLU cc_start: 0.8824 (pm20) cc_final: 0.8536 (pm20)
REVERT: B  168 LEU cc_start: 0.8811 (tp) cc_final: 0.8371 (tt)
REVERT: B  198 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7551 (pp)
REVERT: B  234 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7686 (m-80)
REVERT: B  292 PHE cc_start: 0.8742 (m-10) cc_final: 0.8258 (m-10)
REVERT: H  140 MET cc_start: 0.8055 (mmm) cc_final: 0.7845 (mmm)
REVERT: H  184 SER cc_start: 0.9454 (p) cc_final: 0.9081 (m)
REVERT: C   92 ARG cc_start: 0.6813 (tpt-90) cc_final: 0.5673 (tmm-80)
REVERT: C  107 PHE cc_start: 0.6220 (m-80) cc_final: 0.5972 (m-80)
REVERT: C  355 CYS cc_start: 0.8537 (m) cc_final: 0.8114 (m)
REVERT: D    6 MET cc_start: 0.8304 (tpp) cc_final: 0.7982 (tpp)
  outliers start: 32
  outliers final: 20
  residues processed: 210
  average time/residue: 0.0730
  time to fit residues: 21.4918
Evaluate side-chains
  199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  210 THR
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.187190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.144826 restraints weight = 10876.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.142829 restraints weight = 7246.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.144564 restraints weight = 5874.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.145782 restraints weight = 4651.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146309 restraints weight = 4146.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8594  Z= 0.172
  Angle     :  0.627   8.659  11703  Z= 0.325
  Chirality :  0.044   0.238   1350
  Planarity :  0.004   0.050   1494
  Dihedral  :  4.896  59.553   1208
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 17.78 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1103
  helix:  1.67 (0.26), residues: 402
  sheet: -0.43 (0.31), residues: 276
  loop : -0.03 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  18 
 TYR   0.012   0.002   TYR H 190 
 PHE   0.021   0.002   PHE C  34 
 TRP   0.016   0.001   TRP C  88 
 HIS   0.008   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8590)
  covalent geometry    : angle       0.62720 (11694)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.73063 (    6)
  hydrogen bonds       : bond        0.03685 (  455)
  hydrogen bonds       : angle       5.15893 ( 1284)
  link_TRANS           : bond        0.00164 (    1)
  link_TRANS           : angle       0.84447 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 188
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6513 (mt-10)
REVERT: A  309 GLU cc_start: 0.8793 (pm20) cc_final: 0.8510 (pm20)
REVERT: A  330 GLU cc_start: 0.7798 (tp30) cc_final: 0.7473 (tp30)
REVERT: B   32 GLN cc_start: 0.8558 (mt0) cc_final: 0.8356 (pt0)
REVERT: B  168 LEU cc_start: 0.8870 (tp) cc_final: 0.8425 (tt)
REVERT: B  198 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7652 (pp)
REVERT: B  219 ARG cc_start: 0.6810 (ttm-80) cc_final: 0.6565 (mtm110)
REVERT: B  234 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7638 (m-80)
REVERT: H   37 VAL cc_start: 0.7882 (t) cc_final: 0.6781 (p)
REVERT: H  184 SER cc_start: 0.9436 (p) cc_final: 0.9030 (m)
REVERT: C  107 PHE cc_start: 0.6270 (m-80) cc_final: 0.6004 (m-80)
REVERT: D    6 MET cc_start: 0.8461 (tpp) cc_final: 0.8145 (tpp)
  outliers start: 35
  outliers final: 21
  residues processed: 208
  average time/residue: 0.0856
  time to fit residues: 24.3295
Evaluate side-chains
  198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 82 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 72 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 183 GLN
** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.189286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.146982 restraints weight = 10980.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.145387 restraints weight = 6571.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.147256 restraints weight = 5321.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.148589 restraints weight = 4367.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.148844 restraints weight = 3839.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8594  Z= 0.142
  Angle     :  0.607   8.190  11703  Z= 0.316
  Chirality :  0.044   0.259   1350
  Planarity :  0.004   0.055   1494
  Dihedral  :  4.764  59.951   1208
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.09 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1103
  helix:  1.75 (0.26), residues: 404
  sheet: -0.49 (0.30), residues: 276
  loop : -0.06 (0.33), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 161 
 TYR   0.016   0.001   TYR A 318 
 PHE   0.030   0.002   PHE A 340 
 TRP   0.016   0.001   TRP C  88 
 HIS   0.007   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8590)
  covalent geometry    : angle       0.60713 (11694)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.72299 (    6)
  hydrogen bonds       : bond        0.03551 (  455)
  hydrogen bonds       : angle       5.01662 ( 1284)
  link_TRANS           : bond        0.00241 (    1)
  link_TRANS           : angle       1.07110 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.9055 (p0) cc_final: 0.8852 (p0)
REVERT: A  309 GLU cc_start: 0.8766 (pm20) cc_final: 0.8496 (pm20)
REVERT: B  168 LEU cc_start: 0.8887 (tp) cc_final: 0.8410 (tt)
REVERT: B  198 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7559 (pp)
REVERT: B  234 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7547 (m-80)
REVERT: B  292 PHE cc_start: 0.8706 (m-10) cc_final: 0.8211 (m-10)
REVERT: H   18 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7294 (ttt180)
REVERT: H  184 SER cc_start: 0.9438 (p) cc_final: 0.9014 (m)
REVERT: C  107 PHE cc_start: 0.6184 (m-80) cc_final: 0.5567 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 200
  average time/residue: 0.0852
  time to fit residues: 23.7907
Evaluate side-chains
  200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0010
   chunk 73 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 225 HIS
H 183 GLN
** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.188670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147136 restraints weight = 10888.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145152 restraints weight = 6764.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.146834 restraints weight = 5606.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.148165 restraints weight = 4505.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.148407 restraints weight = 3924.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8594  Z= 0.144
  Angle     :  0.618   9.059  11703  Z= 0.316
  Chirality :  0.043   0.269   1350
  Planarity :  0.004   0.056   1494
  Dihedral  :  4.671  59.085   1208
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.45 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1103
  helix:  1.88 (0.26), residues: 402
  sheet: -0.51 (0.30), residues: 276
  loop : -0.05 (0.33), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 340 
 TYR   0.014   0.001   TYR A 318 
 PHE   0.024   0.002   PHE A 208 
 TRP   0.016   0.001   TRP C  88 
 HIS   0.007   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8590)
  covalent geometry    : angle       0.61750 (11694)
  SS BOND              : bond        0.00142 (    3)
  SS BOND              : angle       0.71200 (    6)
  hydrogen bonds       : bond        0.03490 (  455)
  hydrogen bonds       : angle       5.00321 ( 1284)
  link_TRANS           : bond        0.00202 (    1)
  link_TRANS           : angle       0.97540 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.8797 (pm20) cc_final: 0.8550 (pm20)
REVERT: A  330 GLU cc_start: 0.7811 (tp30) cc_final: 0.7501 (tp30)
REVERT: B   17 GLN cc_start: 0.8173 (pt0) cc_final: 0.7719 (mm-40)
REVERT: B  168 LEU cc_start: 0.8879 (tp) cc_final: 0.8409 (tt)
REVERT: B  198 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7585 (pp)
REVERT: B  234 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7616 (m-80)
REVERT: B  292 PHE cc_start: 0.8676 (m-10) cc_final: 0.8159 (m-10)
REVERT: H  184 SER cc_start: 0.9465 (p) cc_final: 0.9028 (m)
REVERT: C  107 PHE cc_start: 0.5866 (m-80) cc_final: 0.5543 (m-80)
REVERT: D    6 MET cc_start: 0.8498 (tpp) cc_final: 0.7913 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 200
  average time/residue: 0.0926
  time to fit residues: 25.8721
Evaluate side-chains
  192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   72 CYS
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  373 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0030
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0670
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5528

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 225 HIS
H 183 GLN
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.189889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.147796 restraints weight = 10950.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.146793 restraints weight = 6429.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.148417 restraints weight = 5280.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.149774 restraints weight = 4326.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.150059 restraints weight = 3815.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8594  Z= 0.134
  Angle     :  0.612  10.687  11703  Z= 0.314
  Chirality :  0.043   0.284   1350
  Planarity :  0.005   0.094   1494
  Dihedral  :  4.595  58.635   1208
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.33 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1103
  helix:  1.89 (0.26), residues: 404
  sheet: -0.59 (0.30), residues: 274
  loop :  0.01 (0.33), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  27 
 TYR   0.014   0.001   TYR B 111 
 PHE   0.024   0.001   PHE A 340 
 TRP   0.018   0.001   TRP C  88 
 HIS   0.006   0.001   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8590)
  covalent geometry    : angle       0.61191 (11694)
  SS BOND              : bond        0.00250 (    3)
  SS BOND              : angle       0.86256 (    6)
  hydrogen bonds       : bond        0.03486 (  455)
  hydrogen bonds       : angle       4.90112 ( 1284)
  link_TRANS           : bond        0.00206 (    1)
  link_TRANS           : angle       0.94009 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.8757 (pm20) cc_final: 0.8528 (pm20)
REVERT: B   17 GLN cc_start: 0.8084 (pt0) cc_final: 0.7738 (mm-40)
REVERT: B  168 LEU cc_start: 0.8865 (tp) cc_final: 0.8384 (tt)
REVERT: B  198 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7554 (pp)
REVERT: B  234 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7596 (m-80)
REVERT: B  292 PHE cc_start: 0.8616 (m-10) cc_final: 0.8180 (m-10)
REVERT: H  184 SER cc_start: 0.9452 (p) cc_final: 0.8995 (m)
REVERT: D    6 MET cc_start: 0.8470 (tpp) cc_final: 0.7886 (tpp)
  outliers start: 28
  outliers final: 21
  residues processed: 193
  average time/residue: 0.0954
  time to fit residues: 25.6054
Evaluate side-chains
  195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   72 CYS
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  373 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 183 GLN
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.188639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.146142 restraints weight = 10991.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144071 restraints weight = 7409.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146472 restraints weight = 6076.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.147785 restraints weight = 4571.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.148548 restraints weight = 3876.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8594  Z= 0.158
  Angle     :  0.649  10.488  11703  Z= 0.331
  Chirality :  0.044   0.283   1350
  Planarity :  0.004   0.056   1494
  Dihedral  :  4.681  58.532   1208
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.29 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1103
  helix:  1.89 (0.26), residues: 401
  sheet: -0.39 (0.31), residues: 267
  loop : -0.03 (0.33), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  27 
 TYR   0.017   0.002   TYR C 160 
 PHE   0.019   0.002   PHE A 208 
 TRP   0.031   0.002   TRP H  47 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8590)
  covalent geometry    : angle       0.64918 (11694)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.86414 (    6)
  hydrogen bonds       : bond        0.03517 (  455)
  hydrogen bonds       : angle       4.93394 ( 1284)
  link_TRANS           : bond        0.00177 (    1)
  link_TRANS           : angle       0.92634 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  218 ASN cc_start: 0.8444 (p0) cc_final: 0.8186 (p0)
REVERT: A  309 GLU cc_start: 0.8754 (pm20) cc_final: 0.8514 (pm20)
REVERT: B   17 GLN cc_start: 0.8161 (pt0) cc_final: 0.7772 (mm-40)
REVERT: B  168 LEU cc_start: 0.8870 (tp) cc_final: 0.8378 (tt)
REVERT: B  198 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7648 (pp)
REVERT: B  219 ARG cc_start: 0.6854 (ttm-80) cc_final: 0.6645 (mtm110)
REVERT: B  234 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7682 (m-80)
REVERT: B  292 PHE cc_start: 0.8622 (m-10) cc_final: 0.8149 (m-10)
REVERT: H   18 ARG cc_start: 0.7457 (ttt180) cc_final: 0.7154 (ttt180)
REVERT: H   37 VAL cc_start: 0.7676 (t) cc_final: 0.6510 (p)
REVERT: H   47 TRP cc_start: 0.7669 (t60) cc_final: 0.7406 (t60)
REVERT: H  184 SER cc_start: 0.9461 (p) cc_final: 0.9002 (m)
REVERT: D    6 MET cc_start: 0.8507 (tpp) cc_final: 0.7949 (tpp)
  outliers start: 25
  outliers final: 21
  residues processed: 193
  average time/residue: 0.0956
  time to fit residues: 25.3860
Evaluate side-chains
  195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   72 CYS
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  373 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    0.0030
   chunk 24 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0980
   chunk 39 optimal weight:    0.0980
   chunk 83 optimal weight:    8.9990
   chunk 105 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.2990

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 183 GLN
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.192812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.149276 restraints weight = 10784.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.150586 restraints weight = 6336.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.152923 restraints weight = 4651.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.154468 restraints weight = 3549.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.154753 restraints weight = 3139.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8594  Z= 0.120
  Angle     :  0.627  11.300  11703  Z= 0.319
  Chirality :  0.043   0.297   1350
  Planarity :  0.004   0.054   1494
  Dihedral  :  4.506  57.629   1208
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.24 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.87 (0.27), residues: 1103
  helix:  2.01 (0.26), residues: 402
  sheet: -0.45 (0.32), residues: 258
  loop : -0.01 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  27 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.021   0.001   PHE C 151 
 TRP   0.028   0.002   TRP C  88 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8590)
  covalent geometry    : angle       0.62631 (11694)
  SS BOND              : bond        0.00335 (    3)
  SS BOND              : angle       0.83074 (    6)
  hydrogen bonds       : bond        0.03379 (  455)
  hydrogen bonds       : angle       4.75303 ( 1284)
  link_TRANS           : bond        0.00191 (    1)
  link_TRANS           : angle       1.29073 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ASN cc_start: 0.8419 (p0) cc_final: 0.8170 (p0)
REVERT: A  309 GLU cc_start: 0.8704 (pm20) cc_final: 0.8500 (pm20)
REVERT: B   17 GLN cc_start: 0.8154 (pt0) cc_final: 0.7797 (mm-40)
REVERT: B  168 LEU cc_start: 0.8788 (tp) cc_final: 0.8331 (tt)
REVERT: B  198 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7592 (pp)
REVERT: B  234 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7496 (m-80)
REVERT: H   18 ARG cc_start: 0.7465 (ttt180) cc_final: 0.7216 (ttt180)
REVERT: H  184 SER cc_start: 0.9472 (p) cc_final: 0.8974 (m)
REVERT: D    6 MET cc_start: 0.8382 (tpp) cc_final: 0.7864 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 195
  average time/residue: 0.0944
  time to fit residues: 25.4614
Evaluate side-chains
  189 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   72 CYS
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  373 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 93 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 385 GLN
B 259 GLN
H 183 GLN
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.191785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.148718 restraints weight = 10732.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149110 restraints weight = 6129.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.151485 restraints weight = 4682.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152906 restraints weight = 3598.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.153221 restraints weight = 3211.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8594  Z= 0.133
  Angle     :  0.646  12.141  11703  Z= 0.325
  Chirality :  0.044   0.292   1350
  Planarity :  0.004   0.057   1494
  Dihedral  :  4.508  57.540   1208
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 22.32 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 aren not related in a simple way.
  whole:  0.90 (0.27), residues: 1103
  helix:  2.05 (0.26), residues: 399
  sheet: -0.41 (0.32), residues: 262
  loop : -0.00 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 160 
 TYR   0.017   0.001   TYR C 160 
 PHE   0.019   0.002   PHE A 208 
 TRP   0.029   0.002   TRP C  88 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8590)
  covalent geometry    : angle       0.64549 (11694)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.83261 (    6)
  hydrogen bonds       : bond        0.03392 (  455)
  hydrogen bonds       : angle       4.72212 ( 1284)
  link_TRANS           : bond        0.00216 (    1)
  link_TRANS           : angle       1.17414 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1591.31 seconds
wall clock time: 28 minutes 14.39 seconds (1694.39 seconds total)