Starting phenix.real_space_refine
on Mon Apr 28 23:53:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfz_61445/04_2025/9jfz_61445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfz_61445/04_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_61445/04_2025/9jfz_61445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfz_61445/04_2025/9jfz_61445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfz_61445/04_2025/9jfz_61445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfz_61445/04_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.98, per 1000 atoms: 0.73
  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: 2.29
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.98
  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: 2.25

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.22 -     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:             7.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:15.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.320
-------------------------------------------------------------------------------
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  : 0.983 
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: 1.1615
  time to fit residues: 214.5813
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  : 0.801 
-------------------------------------------------------------------------------
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 = 35)----------------|
| 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  : 0.937 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.7689 (m-30) cc_final: 0.7261 (m-30)
REVERT: A  371 ASP cc_start: 0.8209 (t0) cc_final: 0.7935 (t70)
REVERT: B  136 SER cc_start: 0.7834 (t) cc_final: 0.7557 (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: 0.8392 (p) cc_final: 0.8181 (p)
REVERT: C   37 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7012 (tt)
REVERT: R  163 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.5694 (t80)
REVERT: R  225 LEU cc_start: 0.6970 (tp) cc_final: 0.6742 (tp)
  outliers start: 39
  outliers final: 10
  residues processed: 176
  average time/residue: 1.2279
  time to fit residues: 229.7899
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  : 0.844 
-------------------------------------------------------------------------------
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:    3.9990
   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:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:    0.1980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.145282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126679 restraints weight = 11681.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.08
r_work: 0.3550 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.148
  Angle     :  0.564   8.644  11383  Z= 0.303
  Chirality :  0.042   0.146   1272
  Planarity :  0.005   0.086   1462
  Dihedral  :  4.792  54.990   1149
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.54 %
    Favored  : 71.87 %
  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:  0.20 (0.33), residues: 244
  loop : -1.74 (0.27), residues: 390

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05138 (  395)
  hydrogen bonds       : angle       4.33148 ( 1143)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       1.27292 (    8)
  covalent geometry    : bond        0.00329 ( 8379)
  covalent geometry    : angle       0.56292 (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
  191 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7354 (tpp80)
REVERT: A  273 ARG cc_start: 0.7533 (mtp180) cc_final: 0.7228 (mtm110)
REVERT: A  321 ASP cc_start: 0.5850 (OUTLIER) cc_final: 0.5605 (t0)
REVERT: A  368 ASP cc_start: 0.7683 (m-30) cc_final: 0.7208 (m-30)
REVERT: B  136 SER cc_start: 0.7888 (t) cc_final: 0.7634 (p)
REVERT: B  189 SER cc_start: 0.8384 (p) cc_final: 0.8175 (p)
REVERT: C   21 MET cc_start: 0.7513 (tpt) cc_final: 0.7254 (tpt)
REVERT: C   37 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6958 (tt)
REVERT: R   16 ASP cc_start: 0.4724 (OUTLIER) cc_final: 0.4258 (p0)
  outliers start: 40
  outliers final: 18
  residues processed: 180
  average time/residue: 1.1997
  time to fit residues: 229.1838
Evaluate side-chains
  165 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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   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:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0020
   chunk 85 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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
R 217 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.144555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125988 restraints weight = 11572.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.07
r_work: 0.3530 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1874

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= 0.153
  Angle     :  0.572   8.381  11383  Z= 0.308
  Chirality :  0.042   0.146   1272
  Planarity :  0.005   0.077   1462
  Dihedral  :  4.783  53.972   1149
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  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:  0.29 (0.26), residues: 1037
  helix:  1.95 (0.26), residues: 403
  sheet:  0.17 (0.33), residues: 239
  loop : -1.72 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 347 
 PHE   0.018   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        0.05253 (  395)
  hydrogen bonds       : angle       4.29608 ( 1143)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       1.10303 (    8)
  covalent geometry    : bond        0.00345 ( 8379)
  covalent geometry    : angle       0.57163 (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
  190 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7372 (tpp80)
REVERT: A  260 LEU cc_start: 0.8029 (mt) cc_final: 0.7703 (mt)
REVERT: A  321 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5674 (t0)
REVERT: A  368 ASP cc_start: 0.7706 (m-30) cc_final: 0.7284 (m-30)
REVERT: A  371 ASP cc_start: 0.8209 (t0) cc_final: 0.7917 (t70)
REVERT: A  378 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7958 (mt)
REVERT: B   78 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (tptt)
REVERT: B  127 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7598 (mmtt)
REVERT: B  136 SER cc_start: 0.7899 (t) cc_final: 0.7656 (p)
REVERT: B  186 ASP cc_start: 0.7585 (m-30) cc_final: 0.7221 (m-30)
REVERT: B  188 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7935 (mmp)
REVERT: B  189 SER cc_start: 0.8387 (p) cc_final: 0.8175 (p)
REVERT: C   37 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7013 (tt)
REVERT: R  163 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.5553 (t80)
  outliers start: 34
  outliers final: 13
  residues processed: 174
  average time/residue: 1.2638
  time to fit residues: 233.3926
Evaluate side-chains
  169 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
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 A residue  378 LEU
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  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 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:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0000
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.143078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.124517 restraints weight = 11538.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.07
r_work: 0.3529 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8383  Z= 0.173
  Angle     :  0.594   8.197  11383  Z= 0.319
  Chirality :  0.043   0.145   1272
  Planarity :  0.005   0.070   1462
  Dihedral  :  4.873  51.554   1149
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 24.45 %
    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:  0.22 (0.26), residues: 1037
  helix:  1.85 (0.26), residues: 404
  sheet:  0.12 (0.34), residues: 241
  loop : -1.70 (0.27), residues: 392

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   0.018   0.002   TYR R 268 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05531 (  395)
  hydrogen bonds       : angle       4.37409 ( 1143)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       1.06546 (    8)
  covalent geometry    : bond        0.00399 ( 8379)
  covalent geometry    : angle       0.59359 (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
  196 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 154
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7528 (tp30) cc_final: 0.6813 (mp0)
REVERT: A   38 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7435 (tpp80)
REVERT: A  209 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6342 (mp0)
REVERT: A  260 LEU cc_start: 0.8070 (mt) cc_final: 0.7763 (mt)
REVERT: A  321 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5693 (t0)
REVERT: A  368 ASP cc_start: 0.7694 (m-30) cc_final: 0.7219 (m-30)
REVERT: A  371 ASP cc_start: 0.8211 (t0) cc_final: 0.7912 (t70)
REVERT: B  127 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7612 (mmtt)
REVERT: B  136 SER cc_start: 0.7909 (t) cc_final: 0.7680 (p)
REVERT: B  186 ASP cc_start: 0.7606 (m-30) cc_final: 0.7252 (m-30)
REVERT: B  188 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8048 (mmp)
REVERT: B  189 SER cc_start: 0.8396 (p) cc_final: 0.8185 (p)
REVERT: C   37 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6997 (tt)
REVERT: R   16 ASP cc_start: 0.4876 (OUTLIER) cc_final: 0.4359 (p0)
REVERT: R  187 PHE cc_start: 0.8446 (m-80) cc_final: 0.8207 (m-80)
  outliers start: 42
  outliers final: 16
  residues processed: 181
  average time/residue: 1.2476
  time to fit residues: 239.6467
Evaluate side-chains
  173 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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  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   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   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
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:    0.5980
   chunk 95 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 99 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.144418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.125865 restraints weight = 11576.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.08
r_work: 0.3532 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2175

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= 0.150
  Angle     :  0.566   8.011  11383  Z= 0.304
  Chirality :  0.042   0.144   1272
  Planarity :  0.005   0.065   1462
  Dihedral  :  4.759  50.163   1147
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 25.37 %
    Favored  : 70.15 %
  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:  1.94 (0.26), residues: 403
  sheet:  0.22 (0.34), residues: 239
  loop : -1.69 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.016   0.002   PHE R 169 
 TYR   0.018   0.002   TYR R 268 
 ARG   0.010   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05111 (  395)
  hydrogen bonds       : angle       4.24763 ( 1143)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       1.00013 (    8)
  covalent geometry    : bond        0.00339 ( 8379)
  covalent geometry    : angle       0.56599 (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
  193 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7545 (tp30) cc_final: 0.6874 (mp0)
REVERT: A   38 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7361 (tpp80)
REVERT: A  209 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6393 (mp0)
REVERT: A  255 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7009 (mmm-85)
REVERT: A  260 LEU cc_start: 0.8033 (mt) cc_final: 0.7707 (mt)
REVERT: A  321 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5680 (t0)
REVERT: A  368 ASP cc_start: 0.7678 (m-30) cc_final: 0.7193 (m-30)
REVERT: B  127 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7616 (mmtt)
REVERT: B  136 SER cc_start: 0.7893 (t) cc_final: 0.7674 (p)
REVERT: B  146 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8355 (mp)
REVERT: B  155 ASN cc_start: 0.7680 (t0) cc_final: 0.7122 (t0)
REVERT: B  186 ASP cc_start: 0.7604 (m-30) cc_final: 0.7245 (m-30)
REVERT: B  189 SER cc_start: 0.8366 (p) cc_final: 0.8164 (p)
REVERT: C   37 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7014 (tt)
REVERT: R   16 ASP cc_start: 0.5008 (OUTLIER) cc_final: 0.4635 (p0)
REVERT: R  187 PHE cc_start: 0.8443 (m-80) cc_final: 0.8218 (m-80)
  outliers start: 39
  outliers final: 16
  residues processed: 177
  average time/residue: 1.4167
  time to fit residues: 266.3797
Evaluate side-chains
  172 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  292 LEU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  360 GLU
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  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  205 LEU
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:    0.2980
   chunk 38 optimal weight:    0.5980
   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:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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
R  85 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.143348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.124866 restraints weight = 11592.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.07
r_work: 0.3530 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2288

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     :  0.585  10.359  11383  Z= 0.312
  Chirality :  0.043   0.144   1272
  Planarity :  0.005   0.062   1462
  Dihedral  :  4.784  49.171   1147
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 25.72 %
    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:  0.30 (0.26), residues: 1037
  helix:  1.93 (0.27), residues: 402
  sheet:  0.19 (0.34), residues: 239
  loop : -1.67 (0.27), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.016   0.002   PHE R 169 
 TYR   0.018   0.002   TYR R 268 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05285 (  395)
  hydrogen bonds       : angle       4.27009 ( 1143)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       1.04966 (    8)
  covalent geometry    : bond        0.00368 ( 8379)
  covalent geometry    : angle       0.58458 (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
  183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7350 (tpp80)
REVERT: A  209 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6452 (mp0)
REVERT: A  255 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7010 (mmm-85)
REVERT: A  260 LEU cc_start: 0.8064 (mt) cc_final: 0.7746 (mt)
REVERT: A  368 ASP cc_start: 0.7702 (m-30) cc_final: 0.7227 (m-30)
REVERT: B  127 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7647 (mmtt)
REVERT: B  136 SER cc_start: 0.7891 (t) cc_final: 0.7668 (p)
REVERT: B  146 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8371 (mp)
REVERT: B  186 ASP cc_start: 0.7598 (m-30) cc_final: 0.7256 (m-30)
REVERT: B  188 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (mmp)
REVERT: B  189 SER cc_start: 0.8389 (p) cc_final: 0.8170 (p)
REVERT: C   37 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7037 (tt)
  outliers start: 33
  outliers final: 16
  residues processed: 168
  average time/residue: 1.2209
  time to fit residues: 217.5835
Evaluate side-chains
  170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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   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   51 GLU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  205 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0570
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0870
   chunk 97 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 58 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.145343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126644 restraints weight = 11677.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.10
r_work: 0.3548 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2333

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= 0.130
  Angle     :  0.554   9.431  11383  Z= 0.297
  Chirality :  0.042   0.143   1272
  Planarity :  0.005   0.059   1462
  Dihedral  :  4.656  48.929   1147
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 26.41 %
    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:  0.38 (0.26), residues: 1037
  helix:  2.00 (0.27), residues: 404
  sheet:  0.21 (0.33), residues: 239
  loop : -1.64 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.013   0.001   PHE R 169 
 TYR   0.020   0.002   TYR R 268 
 ARG   0.010   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04650 (  395)
  hydrogen bonds       : angle       4.13935 ( 1143)
  SS BOND              : bond        0.00129 (    4)
  SS BOND              : angle       0.89745 (    8)
  covalent geometry    : bond        0.00287 ( 8379)
  covalent geometry    : angle       0.55395 (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
  178 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7582 (tp30) cc_final: 0.6851 (mp0)
REVERT: A   38 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7308 (tpp80)
REVERT: A  209 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6459 (mp0)
REVERT: A  260 LEU cc_start: 0.8018 (mt) cc_final: 0.7697 (mt)
REVERT: A  368 ASP cc_start: 0.7668 (m-30) cc_final: 0.7216 (m-30)
REVERT: B  127 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7643 (mmtt)
REVERT: B  136 SER cc_start: 0.7889 (t) cc_final: 0.7643 (p)
REVERT: B  186 ASP cc_start: 0.7592 (m-30) cc_final: 0.7257 (m-30)
REVERT: C   37 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6956 (tt)
REVERT: R  225 LEU cc_start: 0.6925 (tp) cc_final: 0.6705 (tp)
  outliers start: 26
  outliers final: 18
  residues processed: 165
  average time/residue: 1.2238
  time to fit residues: 214.7867
Evaluate side-chains
  171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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  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  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  205 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 101 optimal weight:    0.0030
   chunk 79 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.3190

-------------------------------------------------------------------------------
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
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.146084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127379 restraints weight = 11766.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.10
r_work: 0.3556 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2390

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= 0.121
  Angle     :  0.546   9.346  11383  Z= 0.292
  Chirality :  0.042   0.148   1272
  Planarity :  0.005   0.059   1462
  Dihedral  :  4.555  48.779   1147
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.98 %
    Favored  : 70.15 %
  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:  0.45 (0.26), residues: 1037
  helix:  2.10 (0.27), residues: 403
  sheet:  0.23 (0.33), residues: 239
  loop : -1.62 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.014   0.001   TYR R 102 
 ARG   0.009   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  395)
  hydrogen bonds       : angle       4.04718 ( 1143)
  SS BOND              : bond        0.00113 (    4)
  SS BOND              : angle       0.82971 (    8)
  covalent geometry    : bond        0.00262 ( 8379)
  covalent geometry    : angle       0.54551 (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
  173 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7593 (tp30) cc_final: 0.6850 (mp0)
REVERT: A   38 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7259 (tpp80)
REVERT: A  209 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6415 (mp0)
REVERT: A  255 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6991 (mmm-85)
REVERT: A  260 LEU cc_start: 0.7967 (mt) cc_final: 0.7554 (mp)
REVERT: A  368 ASP cc_start: 0.7634 (m-30) cc_final: 0.7224 (m-30)
REVERT: A  378 LEU cc_start: 0.8104 (mp) cc_final: 0.7876 (mt)
REVERT: B  127 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7613 (mmtt)
REVERT: B  186 ASP cc_start: 0.7563 (m-30) cc_final: 0.7216 (m-30)
REVERT: B  188 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8009 (mmp)
REVERT: C   37 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6937 (tt)
REVERT: R   65 LEU cc_start: 0.8245 (mt) cc_final: 0.8012 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 160
  average time/residue: 1.2442
  time to fit residues: 211.0094
Evaluate side-chains
  165 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
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 B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0770
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 282 ASN
B 155 ASN
B 239 ASN
B 259 GLN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.144375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.125771 restraints weight = 11524.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.07
r_work: 0.3532 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2426

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   9.453  11383  Z= 0.321
  Chirality :  0.043   0.175   1272
  Planarity :  0.005   0.059   1462
  Dihedral  :  4.699  48.960   1147
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.87 %
    Favored  : 69.92 %
  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:  0.33 (0.26), residues: 1037
  helix:  1.94 (0.26), residues: 403
  sheet:  0.18 (0.33), residues: 239
  loop : -1.65 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   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 268 
 ARG   0.008   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05166 (  395)
  hydrogen bonds       : angle       4.21978 ( 1143)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.94005 (    8)
  covalent geometry    : bond        0.00368 ( 8379)
  covalent geometry    : angle       0.60158 (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
  171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7566 (tp30) cc_final: 0.6832 (mp0)
REVERT: A   38 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7348 (tpp80)
REVERT: A  209 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6446 (mp0)
REVERT: A  255 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7017 (mmm-85)
REVERT: A  260 LEU cc_start: 0.8039 (mt) cc_final: 0.7714 (mt)
REVERT: A  337 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7288 (ttp80)
REVERT: A  368 ASP cc_start: 0.7682 (m-30) cc_final: 0.7244 (m-30)
REVERT: B  127 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7642 (mmtt)
REVERT: B  186 ASP cc_start: 0.7585 (m-30) cc_final: 0.7242 (m-30)
REVERT: B  188 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7970 (mmp)
REVERT: C   37 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7054 (tt)
  outliers start: 28
  outliers final: 15
  residues processed: 159
  average time/residue: 1.2682
  time to fit residues: 213.3435
Evaluate side-chains
  164 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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   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   28 THR
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0270
   chunk 87 optimal weight:    0.0030
   chunk 91 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0770
   chunk 95 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.2206

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

Flipped N/Q/H residues before XYZ refinement:
A 282 ASN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 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 = 0.3917 r_free = 0.3917 target = 0.147183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.128508 restraints weight = 11729.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.10
r_work: 0.3572 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8383  Z= 0.111
  Angle     :  0.541   9.016  11383  Z= 0.288
  Chirality :  0.041   0.152   1272
  Planarity :  0.005   0.058   1462
  Dihedral  :  4.457  48.871   1147
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 28.36 %
    Favored  : 69.69 %
  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:  0.56 (0.26), residues: 1037
  helix:  2.19 (0.27), residues: 403
  sheet:  0.26 (0.33), residues: 244
  loop : -1.56 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 102 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  395)
  hydrogen bonds       : angle       3.96111 ( 1143)
  SS BOND              : bond        0.00106 (    4)
  SS BOND              : angle       0.74766 (    8)
  covalent geometry    : bond        0.00234 ( 8379)
  covalent geometry    : angle       0.54089 (11375)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7252.53 seconds
wall clock time: 126 minutes 35.97 seconds (7595.97 seconds total)