Starting phenix.real_space_refine
on Sun May 11 15:25:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfz_61445/05_2025/9jfz_61445.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
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      52      5.16       5
     C    5200      2.51       5
     N    1424      2.21       5
     O    1522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8198
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1924
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2575
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "C"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 420
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 955
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2324
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 280}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 28
  Time building chain proxies: 5.01, per 1000 atoms: 0.61
  Number of scatterers: 8198
  At special positions: 0
  Unit cell: (93.12, 90.24, 139.2, 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      52     16.00
     O    1522      8.00
     N    1424      7.00
     C    5200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.07
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R   9 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.18
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      40.0% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 4.272A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.726A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.789A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 238'
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.169A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 338
      removed outlier: 3.559A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.756A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 4.303A  pdb=" N   SER R  22 " --> pdb=" O   LEU R  18 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   LEU R  32 " --> pdb=" O   ILE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 76
      removed outlier: 4.328A  pdb=" N   VAL R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 120
      removed outlier: 3.523A  pdb=" N   CYS R  90 " --> pdb=" O   GLY R  86 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   PHE R  95 " --> pdb=" O   LYS R  91 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE R 103 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 150
    Processing helix  chain 'R' and resid 157 through 163
      removed outlier: 3.557A  pdb=" N   TYR R 163 " --> pdb=" O   ARG R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 188
    Processing helix  chain 'R' and resid 190 through 210
    Processing helix  chain 'R' and resid 215 through 254
      removed outlier: 4.148A  pdb=" N   VAL R 233 " --> pdb=" O   LEU R 229 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LEU R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 264
    Processing helix  chain 'R' and resid 265 through 275
    Processing helix  chain 'R' and resid 277 through 287
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 300
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.362A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.940A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.105A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.090A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.701A  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: 7.012A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.102A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.503A  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 232
      removed outlier: 6.490A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.896A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.333A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA N  92 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    395 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2693
        1.34 -     1.46: 1718
        1.46 -     1.58: 3898
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8379
  Sorted by residual:
  bond pdb=" N   PHE R  77 "
       pdb=" CA  PHE R  77 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.03e+00
  bond pdb=" N   VAL R  15 "
       pdb=" CA  VAL R  15 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.09e-02 8.42e+03 8.91e+00
  bond pdb=" N   LEU R  78 "
       pdb=" CA  LEU R  78 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.96e+00
  bond pdb=" N   TYR R  76 "
       pdb=" CA  TYR R  76 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.35e-02 5.49e+03 5.26e+00
  bond pdb=" N   ARG R 202 "
       pdb=" CA  ARG R 202 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.84e+00
  ... (remaining 8374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 11145
        2.06 -     4.13: 196
        4.13 -     6.19: 24
        6.19 -     8.25: 5
        8.25 -    10.32: 5
  Bond angle restraints: 11375
  Sorted by residual:
  angle pdb=" C   ASP R  16 "
        pdb=" CA  ASP R  16 "
        pdb=" CB  ASP R  16 "
      ideal   model   delta    sigma   weight residual
     111.74  101.93    9.81 1.37e+00 5.33e-01 5.13e+01
  angle pdb=" C   CYS R 168 "
        pdb=" CA  CYS R 168 "
        pdb=" CB  CYS R 168 "
      ideal   model   delta    sigma   weight residual
     116.54  110.32    6.22 1.15e+00 7.56e-01 2.92e+01
  angle pdb=" N   LEU R  78 "
        pdb=" CA  LEU R  78 "
        pdb=" C   LEU R  78 "
      ideal   model   delta    sigma   weight residual
     110.80  100.70   10.10 2.13e+00 2.20e-01 2.25e+01
  angle pdb=" N   VAL R  15 "
        pdb=" CA  VAL R  15 "
        pdb=" C   VAL R  15 "
      ideal   model   delta    sigma   weight residual
     113.43  109.21    4.22 1.09e+00 8.42e-01 1.50e+01
  angle pdb=" N   TYR R  76 "
        pdb=" CA  TYR R  76 "
        pdb=" C   TYR R  76 "
      ideal   model   delta    sigma   weight residual
     113.01  108.63    4.38 1.20e+00 6.94e-01 1.33e+01
  ... (remaining 11370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 4283
       16.40 -    32.80: 471
       32.80 -    49.20: 147
       49.20 -    65.60: 49
       65.60 -    82.00: 8
  Dihedral angle restraints: 4958
    sinusoidal: 1906
      harmonic: 3052
  Sorted by residual:
  dihedral pdb=" CB  CYS R  90 "
           pdb=" SG  CYS R  90 "
           pdb=" SG  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.71   68.71     1      1.00e+01 1.00e-02 6.11e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.79   55.79     1      1.00e+01 1.00e-02 4.20e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.25   53.75     1      1.00e+01 1.00e-02 3.92e+01
  ... (remaining 4955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1100
       0.065 -    0.129: 166
       0.129 -    0.194: 4
       0.194 -    0.258: 0
       0.258 -    0.323: 2
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  LEU R  78 "
            pdb=" N   LEU R  78 "
            pdb=" C   LEU R  78 "
            pdb=" CB  LEU R  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  ASP R  16 "
            pdb=" N   ASP R  16 "
            pdb=" C   ASP R  16 "
            pdb=" CB  ASP R  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  VAL R  15 "
            pdb=" N   VAL R  15 "
            pdb=" C   VAL R  15 "
            pdb=" CB  VAL R  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 1269 not shown)

  Planarity restraints: 1462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "    0.101 5.00e-02 4.00e+02   1.51e-01 3.67e+01
        pdb=" N   PRO N  88 "   -0.262 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "    0.084 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "    0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "   -0.059 5.00e-02 4.00e+02   8.86e-02 1.26e+01
        pdb=" N   PRO C  53 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R  48 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.25e+00
        pdb=" C   GLN R  48 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLN R  48 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG R  49 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1459 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 717
        2.74 -     3.28: 7829
        3.28 -     3.82: 13041
        3.82 -     4.36: 14808
        4.36 -     4.90: 26535
  Nonbonded interactions: 62930
  Sorted by model distance:
  nonbonded pdb=" N   GLU R 157 "
            pdb=" OE1 GLU R 157 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" CG1 VAL A 247 "
            pdb=" OD1 ASN A 282 "
     model   vdw
     2.218 3.460
  nonbonded pdb=" N   GLU R  51 "
            pdb=" OE1 GLU R  51 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASN R 290 "
            pdb=" N   ALA R 293 "
     model   vdw
     2.256 3.120
  ... (remaining 62925 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.520
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.220
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8383  Z= 0.177
  Angle     :  0.695  13.728  11383  Z= 0.392
  Chirality :  0.044   0.323   1272
  Planarity :  0.007   0.151   1462
  Dihedral  : 16.113  81.996   2976
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 25.72 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1037
  helix:  1.70 (0.27), residues: 393
  sheet:  0.41 (0.34), residues: 223
  loop : -1.58 (0.27), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 177 
 HIS   0.005   0.001   HIS R  85 
 PHE   0.026   0.002   PHE R 172 
 TYR   0.020   0.002   TYR N  60 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13626 (  395)
  hydrogen bonds       : angle       5.30091 ( 1143)
  SS BOND              : bond        0.01906 (    4)
  SS BOND              : angle       6.55238 (    8)
  covalent geometry    : bond        0.00347 ( 8379)
  covalent geometry    : angle       0.67271 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 171
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6422 (tpp80)
REVERT: A  209 GLU cc_start: 0.7574 (tp30) cc_final: 0.7337 (tp30)
REVERT: A  273 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6876 (mtp180)
REVERT: A  282 ASN cc_start: 0.7670 (m110) cc_final: 0.7338 (m110)
REVERT: A  297 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7864 (mtpt)
REVERT: A  368 ASP cc_start: 0.7491 (m-30) cc_final: 0.7158 (m-30)
REVERT: B   59 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7780 (t80)
REVERT: B   78 LYS cc_start: 0.8524 (tttp) cc_final: 0.8276 (tttt)
REVERT: B  111 TYR cc_start: 0.8174 (m-80) cc_final: 0.7847 (m-80)
  outliers start: 5
  outliers final: 4
  residues processed: 174
  average time/residue: 1.1628
  time to fit residues: 215.0795
Evaluate side-chains
  160 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 155
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   16 ASP
Chi-restraints excluded: chain R residue  105 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 176 GLN
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.143658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125209 restraints weight = 11520.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.05
r_work: 0.3529 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8383  Z= 0.213
  Angle     :  0.654   8.376  11383  Z= 0.351
  Chirality :  0.045   0.150   1272
  Planarity :  0.006   0.110   1462
  Dihedral  :  5.467  56.176   1153
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 24.00 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1037
  helix:  1.72 (0.26), residues: 403
  sheet:  0.25 (0.34), residues: 233
  loop : -1.72 (0.27), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.013   0.002   HIS A 347 
 PHE   0.024   0.002   PHE R 167 
 TYR   0.021   0.002   TYR R 251 
 ARG   0.006   0.001   ARG N  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06348 (  395)
  hydrogen bonds       : angle       4.62129 ( 1143)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       1.27050 (    8)
  covalent geometry    : bond        0.00495 ( 8379)
  covalent geometry    : angle       0.65298 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.7690 (m-30) cc_final: 0.7261 (m-30)
REVERT: A  371 ASP cc_start: 0.8208 (t0) cc_final: 0.7935 (t70)
REVERT: B  136 SER cc_start: 0.7834 (t) cc_final: 0.7556 (p)
REVERT: B  171 ILE cc_start: 0.8139 (mm) cc_final: 0.7923 (mt)
REVERT: B  188 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7934 (mmp)
REVERT: B  189 SER cc_start: 0.8393 (p) cc_final: 0.8182 (p)
REVERT: C   37 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7011 (tt)
REVERT: R  163 TYR cc_start: 0.5896 (OUTLIER) cc_final: 0.5694 (t80)
REVERT: R  225 LEU cc_start: 0.6965 (tp) cc_final: 0.6738 (tp)
  outliers start: 39
  outliers final: 10
  residues processed: 176
  average time/residue: 1.1582
  time to fit residues: 216.8227
Evaluate side-chains
  163 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  163 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 176 GLN
B 237 ASN
B 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.145352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126684 restraints weight = 11685.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.09
r_work: 0.3549 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8383  Z= 0.144
  Angle     :  0.563   9.006  11383  Z= 0.302
  Chirality :  0.042   0.146   1272
  Planarity :  0.005   0.086   1462
  Dihedral  :  4.793  55.110   1149
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.54 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1037
  helix:  1.92 (0.26), residues: 403
  sheet:  0.19 (0.33), residues: 244
  loop : -1.74 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 347 
 PHE   0.018   0.002   PHE R 169 
 TYR   0.017   0.002   TYR R 268 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05130 (  395)
  hydrogen bonds       : angle       4.33735 ( 1143)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       1.20829 (    8)
  covalent geometry    : bond        0.00319 ( 8379)
  covalent geometry    : angle       0.56263 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7343 (tpp80)
REVERT: A  273 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7229 (mtm110)
REVERT: A  321 ASP cc_start: 0.5851 (OUTLIER) cc_final: 0.5598 (t0)
REVERT: A  368 ASP cc_start: 0.7682 (m-30) cc_final: 0.7208 (m-30)
REVERT: B  136 SER cc_start: 0.7894 (t) cc_final: 0.7636 (p)
REVERT: B  189 SER cc_start: 0.8385 (p) cc_final: 0.8181 (p)
REVERT: C   21 MET cc_start: 0.7523 (tpt) cc_final: 0.7267 (tpt)
REVERT: C   37 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6933 (tt)
REVERT: R   16 ASP cc_start: 0.4549 (OUTLIER) cc_final: 0.4081 (p0)
  outliers start: 39
  outliers final: 19
  residues processed: 178
  average time/residue: 1.1623
  time to fit residues: 219.8021
Evaluate side-chains
  166 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   16 ASP
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  233 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0040
   chunk 85 optimal weight:    0.0050
   chunk 28 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.4206

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
B 155 ASN
B 176 GLN
B 239 ASN
N  31 ASN
R 217 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.144744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126259 restraints weight = 11555.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.06
r_work: 0.3542 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8383  Z= 0.136
  Angle     :  0.550   8.393  11383  Z= 0.296
  Chirality :  0.042   0.144   1272
  Planarity :  0.005   0.076   1462
  Dihedral  :  4.701  54.132   1149
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 24.91 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.26), residues: 1037
  helix:  2.01 (0.26), residues: 404
  sheet:  0.17 (0.33), residues: 239
  loop : -1.70 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 347 
 PHE   0.016   0.002   PHE R 169 
 TYR   0.020   0.002   TYR R 102 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04893 (  395)
  hydrogen bonds       : angle       4.21937 ( 1143)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       1.00201 (    8)
  covalent geometry    : bond        0.00302 ( 8379)
  covalent geometry    : angle       0.54974 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7328 (tpp80)
REVERT: A  260 LEU cc_start: 0.8006 (mt) cc_final: 0.7669 (mt)
REVERT: A  321 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.5641 (t0)
REVERT: A  368 ASP cc_start: 0.7686 (m-30) cc_final: 0.7247 (m-30)
REVERT: A  371 ASP cc_start: 0.8203 (t0) cc_final: 0.7832 (t70)
REVERT: B   78 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8556 (tptt)
REVERT: B  127 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7585 (mmtt)
REVERT: B  136 SER cc_start: 0.7890 (t) cc_final: 0.7635 (p)
REVERT: B  189 SER cc_start: 0.8375 (p) cc_final: 0.8163 (p)
REVERT: C   37 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6982 (tt)
REVERT: R  163 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.5534 (t80)
  outliers start: 34
  outliers final: 13
  residues processed: 175
  average time/residue: 1.1929
  time to fit residues: 221.6632
Evaluate side-chains
  171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  163 TYR
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  205 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0870
   chunk 39 optimal weight:    0.8980
   chunk 88 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 176 GLN
B 239 ASN
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.144377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.125844 restraints weight = 11530.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.08
r_work: 0.3534 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8383  Z= 0.158
  Angle     :  0.572   8.182  11383  Z= 0.307
  Chirality :  0.043   0.145   1272
  Planarity :  0.005   0.068   1462
  Dihedral  :  4.755  51.895   1147
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 24.57 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1037
  helix:  1.90 (0.26), residues: 405
  sheet:  0.20 (0.34), residues: 239
  loop : -1.67 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.016   0.002   PHE R 169 
 TYR   0.019   0.002   TYR R 102 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05295 (  395)
  hydrogen bonds       : angle       4.27214 ( 1143)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       1.04423 (    8)
  covalent geometry    : bond        0.00359 ( 8379)
  covalent geometry    : angle       0.57144 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 155
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7414 (tpp80)
REVERT: A  260 LEU cc_start: 0.8036 (mt) cc_final: 0.7720 (mt)
REVERT: A  282 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7702 (m-40)
REVERT: A  368 ASP cc_start: 0.7678 (m-30) cc_final: 0.7225 (m-30)
REVERT: B  127 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7624 (mmtt)
REVERT: B  136 SER cc_start: 0.7894 (t) cc_final: 0.7653 (p)
REVERT: B  146 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (mp)
REVERT: B  186 ASP cc_start: 0.7613 (m-30) cc_final: 0.7258 (m-30)
REVERT: B  188 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7962 (mmp)
REVERT: B  189 SER cc_start: 0.8399 (p) cc_final: 0.8184 (p)
REVERT: C   37 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6979 (tt)
REVERT: R   16 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4300 (p0)
  outliers start: 42
  outliers final: 16
  residues processed: 182
  average time/residue: 1.0995
  time to fit residues: 213.1933
Evaluate side-chains
  171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   16 ASP
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0970
   chunk 99 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 176 GLN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.143351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.124836 restraints weight = 11574.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.07
r_work: 0.3528 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8383  Z= 0.164
  Angle     :  0.581  10.231  11383  Z= 0.312
  Chirality :  0.043   0.145   1272
  Planarity :  0.005   0.063   1462
  Dihedral  :  4.775  50.464   1147
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 25.03 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1037
  helix:  1.90 (0.26), residues: 404
  sheet:  0.22 (0.34), residues: 239
  loop : -1.68 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.019   0.002   PHE R 169 
 TYR   0.017   0.002   TYR R 268 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05338 (  395)
  hydrogen bonds       : angle       4.25427 ( 1143)
  SS BOND              : bond        0.00168 (    4)
  SS BOND              : angle       1.02639 (    8)
  covalent geometry    : bond        0.00376 ( 8379)
  covalent geometry    : angle       0.58032 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 152
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7429 (tpp80)
REVERT: A  209 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6411 (mp0)
REVERT: A  260 LEU cc_start: 0.8051 (mt) cc_final: 0.7730 (mt)
REVERT: A  368 ASP cc_start: 0.7697 (m-30) cc_final: 0.7220 (m-30)
REVERT: B  127 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7631 (mmtt)
REVERT: B  136 SER cc_start: 0.7886 (t) cc_final: 0.7663 (p)
REVERT: B  146 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8356 (mp)
REVERT: B  186 ASP cc_start: 0.7594 (m-30) cc_final: 0.7244 (m-30)
REVERT: B  188 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7947 (mmp)
REVERT: B  189 SER cc_start: 0.8388 (p) cc_final: 0.8175 (p)
REVERT: C   37 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7050 (tt)
REVERT: R   16 ASP cc_start: 0.4939 (OUTLIER) cc_final: 0.4501 (p0)
  outliers start: 37
  outliers final: 19
  residues processed: 173
  average time/residue: 1.1784
  time to fit residues: 216.3232
Evaluate side-chains
  174 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   16 ASP
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 38 optimal weight:    0.2980
   chunk 0 optimal weight:    5.9990
   chunk 87 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 176 GLN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.143934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125527 restraints weight = 11597.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.07
r_work: 0.3536 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8383  Z= 0.146
  Angle     :  0.564   9.448  11383  Z= 0.302
  Chirality :  0.042   0.144   1272
  Planarity :  0.005   0.060   1462
  Dihedral  :  4.694  49.238   1147
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 25.72 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1037
  helix:  1.95 (0.27), residues: 404
  sheet:  0.25 (0.34), residues: 239
  loop : -1.62 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.015   0.002   PHE R 169 
 TYR   0.016   0.002   TYR R 102 
 ARG   0.010   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05018 (  395)
  hydrogen bonds       : angle       4.18441 ( 1143)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.98642 (    8)
  covalent geometry    : bond        0.00330 ( 8379)
  covalent geometry    : angle       0.56388 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 151
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7582 (tp30) cc_final: 0.6885 (mp0)
REVERT: A   38 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7344 (tpp80)
REVERT: A  209 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6443 (mp0)
REVERT: A  260 LEU cc_start: 0.8047 (mt) cc_final: 0.7721 (mt)
REVERT: A  368 ASP cc_start: 0.7687 (m-30) cc_final: 0.7242 (m-30)
REVERT: B  127 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7656 (mmtt)
REVERT: B  136 SER cc_start: 0.7889 (t) cc_final: 0.7646 (p)
REVERT: B  146 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (mp)
REVERT: B  155 ASN cc_start: 0.7695 (t0) cc_final: 0.7147 (t0)
REVERT: B  186 ASP cc_start: 0.7605 (m-30) cc_final: 0.7254 (m-30)
REVERT: B  188 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7968 (mmp)
REVERT: B  189 SER cc_start: 0.8373 (p) cc_final: 0.8166 (p)
REVERT: C   37 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7036 (tt)
REVERT: R   16 ASP cc_start: 0.5202 (OUTLIER) cc_final: 0.4948 (p0)
  outliers start: 34
  outliers final: 19
  residues processed: 169
  average time/residue: 1.1763
  time to fit residues: 210.9230
Evaluate side-chains
  173 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   16 ASP
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 73 optimal weight:    0.3980
   chunk 60 optimal weight:    0.0010
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 98 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125560 restraints weight = 11666.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.08
r_work: 0.3536 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8383  Z= 0.147
  Angle     :  0.568   9.217  11383  Z= 0.303
  Chirality :  0.042   0.144   1272
  Planarity :  0.005   0.060   1462
  Dihedral  :  4.692  48.883   1147
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.41 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1037
  helix:  1.95 (0.27), residues: 403
  sheet:  0.26 (0.34), residues: 239
  loop : -1.65 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.015   0.002   PHE R 169 
 TYR   0.017   0.002   TYR R 268 
 ARG   0.007   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  395)
  hydrogen bonds       : angle       4.18265 ( 1143)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       0.95155 (    8)
  covalent geometry    : bond        0.00333 ( 8379)
  covalent geometry    : angle       0.56725 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7576 (tp30) cc_final: 0.6878 (mp0)
REVERT: A   38 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7342 (tpp80)
REVERT: A  209 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6470 (mp0)
REVERT: A  260 LEU cc_start: 0.8051 (mt) cc_final: 0.7729 (mt)
REVERT: A  368 ASP cc_start: 0.7691 (m-30) cc_final: 0.7246 (m-30)
REVERT: B  127 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7665 (mmtt)
REVERT: B  136 SER cc_start: 0.7895 (t) cc_final: 0.7656 (p)
REVERT: B  186 ASP cc_start: 0.7591 (m-30) cc_final: 0.7248 (m-30)
REVERT: B  188 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7954 (mmp)
REVERT: B  189 SER cc_start: 0.8370 (p) cc_final: 0.8157 (p)
REVERT: C   37 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7024 (tt)
REVERT: R  250 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6727 (pp)
  outliers start: 27
  outliers final: 19
  residues processed: 159
  average time/residue: 1.1762
  time to fit residues: 198.8507
Evaluate side-chains
  167 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  242 VAL
Chi-restraints excluded: chain R residue  250 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0870
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0070
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.144498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.125870 restraints weight = 11740.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.10
r_work: 0.3543 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8383  Z= 0.142
  Angle     :  0.571   9.053  11383  Z= 0.306
  Chirality :  0.043   0.153   1272
  Planarity :  0.005   0.058   1462
  Dihedral  :  4.671  48.843   1147
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.41 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1037
  helix:  1.97 (0.27), residues: 403
  sheet:  0.25 (0.34), residues: 239
  loop : -1.65 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.013   0.002   PHE R 169 
 TYR   0.020   0.002   TYR R 268 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04849 (  395)
  hydrogen bonds       : angle       4.15096 ( 1143)
  SS BOND              : bond        0.00137 (    4)
  SS BOND              : angle       0.90215 (    8)
  covalent geometry    : bond        0.00317 ( 8379)
  covalent geometry    : angle       0.57114 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7587 (tp30) cc_final: 0.6920 (mp0)
REVERT: A   38 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7315 (tpp80)
REVERT: A  209 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6460 (mp0)
REVERT: A  260 LEU cc_start: 0.8031 (mt) cc_final: 0.7638 (mp)
REVERT: A  368 ASP cc_start: 0.7687 (m-30) cc_final: 0.7240 (m-30)
REVERT: B  127 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7647 (mmtt)
REVERT: B  136 SER cc_start: 0.7907 (t) cc_final: 0.7668 (p)
REVERT: B  186 ASP cc_start: 0.7604 (m-30) cc_final: 0.7258 (m-30)
REVERT: B  188 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7992 (mmp)
REVERT: B  259 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6284 (mt0)
REVERT: C   37 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7003 (tt)
REVERT: R  185 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7112 (ttm170)
REVERT: R  250 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6738 (pp)
  outliers start: 28
  outliers final: 19
  residues processed: 165
  average time/residue: 1.2457
  time to fit residues: 217.8926
Evaluate side-chains
  170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  242 VAL
Chi-restraints excluded: chain R residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 82 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 237 ASN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.143675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.125190 restraints weight = 11509.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.08
r_work: 0.3535 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8383  Z= 0.155
  Angle     :  0.595   9.112  11383  Z= 0.318
  Chirality :  0.043   0.180   1272
  Planarity :  0.005   0.058   1462
  Dihedral  :  4.718  48.829   1147
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.78 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1037
  helix:  1.89 (0.27), residues: 403
  sheet:  0.23 (0.34), residues: 239
  loop : -1.65 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.014   0.002   PHE R 169 
 TYR   0.018   0.002   TYR R 268 
 ARG   0.011   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05119 (  395)
  hydrogen bonds       : angle       4.22378 ( 1143)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       0.93051 (    8)
  covalent geometry    : bond        0.00353 ( 8379)
  covalent geometry    : angle       0.59506 (11375)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7572 (tp30) cc_final: 0.6901 (mp0)
REVERT: A   38 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7361 (tpp80)
REVERT: A  209 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6467 (mp0)
REVERT: A  260 LEU cc_start: 0.8044 (mt) cc_final: 0.7733 (mt)
REVERT: A  337 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7267 (ttp80)
REVERT: A  368 ASP cc_start: 0.7697 (m-30) cc_final: 0.7259 (m-30)
REVERT: B  127 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7648 (mmtt)
REVERT: B  136 SER cc_start: 0.7894 (t) cc_final: 0.7664 (p)
REVERT: B  186 ASP cc_start: 0.7593 (m-30) cc_final: 0.7254 (m-30)
REVERT: B  188 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7995 (mmp)
REVERT: B  259 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6258 (mt0)
REVERT: C   37 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7025 (tt)
REVERT: R  250 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6806 (pp)
  outliers start: 25
  outliers final: 17
  residues processed: 154
  average time/residue: 1.2929
  time to fit residues: 210.6874
Evaluate side-chains
  164 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  242 VAL
Chi-restraints excluded: chain R residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0570
   chunk 95 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 239 ASN
N  31 ASN
R  85 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.143644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125124 restraints weight = 11652.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.08
r_work: 0.3535 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8383  Z= 0.161
  Angle     :  0.602   9.017  11383  Z= 0.321
  Chirality :  0.043   0.186   1272
  Planarity :  0.005   0.057   1462
  Dihedral  :  4.751  48.858   1147
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 27.32 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 1037
  helix:  1.88 (0.27), residues: 403
  sheet:  0.22 (0.34), residues: 239
  loop : -1.66 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.015   0.002   PHE R 169 
 TYR   0.019   0.002   TYR R 268 
 ARG   0.011   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05187 (  395)
  hydrogen bonds       : angle       4.24243 ( 1143)
  SS BOND              : bond        0.00157 (    4)
  SS BOND              : angle       0.94179 (    8)
  covalent geometry    : bond        0.00368 ( 8379)
  covalent geometry    : angle       0.60128 (11375)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6456.44 seconds
wall clock time: 111 minutes 40.09 seconds (6700.09 seconds total)