Starting phenix.real_space_refine
on Wed Mar 12 01:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzg_38795/03_2025/8xzg_38795.cif"
  }
  resolution = 3.2
  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=  -0.000 sd=   0.013
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      61      5.16       5
     C    4572      2.51       5
     N    1222      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7172
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1737
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2528
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "L"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 107
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 3, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2356
          Classifications: {'peptide': 300}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 288}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 4.67, per 1000 atoms: 0.65
  Number of scatterers: 7172
  At special positions: 0
  Unit cell: (78.078, 120.666, 118.638, 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      61     16.00
     O    1317      8.00
     N    1222      7.00
     C    4572      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.02

  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: 1.95
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      44.8% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.941A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.524A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.114A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.509A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.019A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.703A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.899A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'G' and resid 6 through 22
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.717A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 27 through 53
      Proline residue:  R  32  - end of helix
      removed outlier: 3.942A  pdb=" N   GLY R  47 " --> pdb=" O   THR R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 81
      removed outlier: 3.841A  pdb=" N   THR R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 90
      removed outlier: 3.517A  pdb=" N   TYR R  90 " --> pdb=" O   ALA R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 132
      removed outlier: 4.168A  pdb=" N   SER R 106 " --> pdb=" O   CYS R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 144
      removed outlier: 3.859A  pdb=" N   ARG R 141 " --> pdb=" O   ASN R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 148 through 161
    Processing helix  chain 'R' and resid 162 through 165
    Processing helix  chain 'R' and resid 190 through 192
      No H-bonds generated for 'chain 'R' and resid 190 through 192'
    Processing helix  chain 'R' and resid 193 through 210
      removed outlier: 3.522A  pdb=" N   TRP R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR R 206 " --> pdb=" O   GLY R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 240 through 275
      removed outlier: 4.072A  pdb=" N   ARG R 245 " --> pdb=" O   ARG R 241 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU R 246 " --> pdb=" O   LYS R 242 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU R 247 " --> pdb=" O   ARG R 243 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   PHE R 257 " --> pdb=" O   LEU R 253 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET R 262 " --> pdb=" O   ALA R 258 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 283 through 298
      Proline residue:  R 292  - end of helix
      removed outlier: 4.224A  pdb=" N   CYS R 296 " --> pdb=" O   PRO R 292 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER R 298 " --> pdb=" O   CYS R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 305
    Processing helix  chain 'R' and resid 305 through 310
    Processing helix  chain 'R' and resid 313 through 327
      removed outlier: 3.739A  pdb=" N   ARG R 317 " --> pdb=" O   ASP R 313 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLY R 327 " --> pdb=" O   MET R 323 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.819A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.690A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 6.844A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114
      removed outlier: 5.969A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.576A  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
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190
      removed outlier: 6.543A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.865A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.691A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 168 through 172
      removed outlier: 3.533A  pdb=" N   THR R 169 " --> pdb=" O   TYR R 182 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR R 182 " --> pdb=" O   THR R 169 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    957 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: 2.08

  Time building geometry restraints manager: 2.31 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: 2259
        1.34 -     1.45: 1178
        1.45 -     1.57: 3794
        1.57 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 7319
  Sorted by residual:
  bond pdb=" N   PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.463 -0.118 2.00e-02 2.50e+03 3.48e+01
  bond pdb=" N   TRP R 279 "
       pdb=" CA  TRP R 279 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 9.20e-03 1.18e+04 1.37e+01
  bond pdb=" N   ILE R 290 "
       pdb=" CA  ILE R 290 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.09e-02 8.42e+03 1.23e+01
  bond pdb=" N   VAL R  79 "
       pdb=" CA  VAL R  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.037 1.22e-02 6.72e+03 9.37e+00
  bond pdb=" N   VAL R  80 "
       pdb=" CA  VAL R  80 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.12e+00
  ... (remaining 7314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 9516
        2.02 -     4.05: 355
        4.05 -     6.07: 34
        6.07 -     8.09: 6
        8.09 -    10.11: 1
  Bond angle restraints: 9912
  Sorted by residual:
  angle pdb=" N   HIS R 231 "
        pdb=" CA  HIS R 231 "
        pdb=" C   HIS R 231 "
      ideal   model   delta    sigma   weight residual
     111.36  117.00   -5.64 1.09e+00 8.42e-01 2.68e+01
  angle pdb=" N   THR R  99 "
        pdb=" CA  THR R  99 "
        pdb=" C   THR R  99 "
      ideal   model   delta    sigma   weight residual
     111.71  105.87    5.84 1.15e+00 7.56e-01 2.58e+01
  angle pdb=" O   ILE R  31 "
        pdb=" C   ILE R  31 "
        pdb=" N   PRO R  32 "
      ideal   model   delta    sigma   weight residual
     120.42  123.50   -3.08 6.40e-01 2.44e+00 2.31e+01
  angle pdb=" N   LYS R 242 "
        pdb=" CA  LYS R 242 "
        pdb=" C   LYS R 242 "
      ideal   model   delta    sigma   weight residual
     113.17  107.68    5.49 1.26e+00 6.30e-01 1.90e+01
  angle pdb=" C   TRP R 279 "
        pdb=" N   PRO R 280 "
        pdb=" CA  PRO R 280 "
      ideal   model   delta    sigma   weight residual
     119.84  124.99   -5.15 1.25e+00 6.40e-01 1.70e+01
  ... (remaining 9907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 3844
       17.18 -    34.36: 419
       34.36 -    51.53: 69
       51.53 -    68.71: 7
       68.71 -    85.89: 4
  Dihedral angle restraints: 4343
    sinusoidal: 1669
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" CA  PHE B 199 "
           pdb=" C   PHE B 199 "
           pdb=" N   VAL B 200 "
           pdb=" CA  VAL B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.82   25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  PHE B 241 "
           pdb=" C   PHE B 241 "
           pdb=" N   ALA B 242 "
           pdb=" CA  ALA B 242 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.67   23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.96   18.04     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4340 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 834
       0.054 -    0.108: 226
       0.108 -    0.162: 62
       0.162 -    0.216: 12
       0.216 -    0.270: 1
  Chirality restraints: 1135
  Sorted by residual:
  chirality pdb=" CA  HIS R 231 "
            pdb=" N   HIS R 231 "
            pdb=" C   HIS R 231 "
            pdb=" CB  HIS R 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CA  LEU R  71 "
            pdb=" N   LEU R  71 "
            pdb=" C   LEU R  71 "
            pdb=" CB  LEU R  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  LEU R 120 "
            pdb=" N   LEU R 120 "
            pdb=" C   LEU R 120 "
            pdb=" CB  LEU R 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.43e-01
  ... (remaining 1132 not shown)

  Planarity restraints: 1247
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 230 "    0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   GLY R 230 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   GLY R 230 "    0.021 2.00e-02 2.50e+03
        pdb=" N   HIS R 231 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  60 "   -0.014 2.00e-02 2.50e+03   2.76e-02 7.62e+00
        pdb=" C   ALA B  60 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ALA B  60 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET B  61 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  83 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.18e+00
        pdb=" C   ASP B  83 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASP B  83 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER B  84 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1244 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 433
        2.72 -     3.26: 6935
        3.26 -     3.81: 10928
        3.81 -     4.35: 13336
        4.35 -     4.90: 23771
  Nonbonded interactions: 55403
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN R  46 "
            pdb=" OD2 ASP R  75 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" O   THR R 295 "
            pdb=" CE1 TYR R 299 "
     model   vdw
     2.209 3.340
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH2 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.279 3.120
  ... (remaining 55398 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.430
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
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      :  0.008   0.118   7319  Z= 0.514
  Angle     :  0.881  10.115   9912  Z= 0.580
  Chirality :  0.055   0.270   1135
  Planarity :  0.005   0.047   1247
  Dihedral  : 14.038  85.891   2606
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.11 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.08 %
    Favored  : 89.36 %
  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: -2.72 (0.25), residues: 900
  helix: -0.45 (0.25), residues: 382
  sheet: -3.04 (0.29), residues: 169
  loop : -2.59 (0.28), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.017   0.002   PHE G  61 
 TYR   0.009   0.001   TYR B 124 
 ARG   0.004   0.000   ARG R  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7726 (mttt) cc_final: 0.7488 (mttp)
REVERT: A  251 ASP cc_start: 0.8791 (t70) cc_final: 0.8575 (t0)
REVERT: A  260 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (t)
REVERT: B  118 ASP cc_start: 0.7505 (t0) cc_final: 0.7245 (t0)
REVERT: B  129 ARG cc_start: 0.7139 (tpt90) cc_final: 0.6346 (mtp-110)
REVERT: B  214 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6712 (mmt180)
REVERT: B  226 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7847 (mt-10)
REVERT: R   31 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4547 (mm)
REVERT: R  323 MET cc_start: 0.6677 (mmm) cc_final: 0.5828 (mtt)
  outliers start: 12
  outliers final: 3
  residues processed: 120
  average time/residue: 0.2582
  time to fit residues: 39.2304
Evaluate side-chains
  91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  119 CYS
Chi-restraints excluded: chain R residue  207 THR
Chi-restraints excluded: chain R residue  253 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 68 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 52 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 244 HIS
B  91 HIS
B 155 ASN
B 183 HIS
G  24 ASN
L   7 HIS
** R  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 289 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.183785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.134626 restraints weight = 7524.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.40
r_work: 0.3366 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7319  Z= 0.188
  Angle     :  0.553   6.012   9912  Z= 0.293
  Chirality :  0.042   0.147   1135
  Planarity :  0.004   0.045   1247
  Dihedral  :  5.120  50.435    999
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.23 %
    Favored  : 85.08 %
  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: -1.46 (0.27), residues: 900
  helix:  0.62 (0.27), residues: 397
  sheet: -2.55 (0.31), residues: 179
  loop : -1.91 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  95 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.025   0.001   PHE R  39 
 TYR   0.012   0.001   TYR R  35 
 ARG   0.006   0.001   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 1.069 
Fit side-chains
REVERT: B  118 ASP cc_start: 0.8030 (t0) cc_final: 0.7767 (t0)
REVERT: B  129 ARG cc_start: 0.7200 (tpt90) cc_final: 0.6039 (mtp-110)
REVERT: B  152 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: B  200 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8254 (m)
REVERT: B  214 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6885 (mmt180)
REVERT: B  226 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8395 (mt-10)
REVERT: B  234 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (m-80)
REVERT: B  258 ASP cc_start: 0.6712 (t70) cc_final: 0.5971 (t70)
REVERT: R  323 MET cc_start: 0.6654 (mmm) cc_final: 0.5862 (mtt)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.2626
  time to fit residues: 33.8076
Evaluate side-chains
  88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue  253 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
R  46 ASN
R 231 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.185017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.134709 restraints weight = 7654.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.49
r_work: 0.3356 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7319  Z= 0.185
  Angle     :  0.494   5.325   9912  Z= 0.260
  Chirality :  0.041   0.142   1135
  Planarity :  0.004   0.041   1247
  Dihedral  :  4.450  48.920    994
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.05 %
    Favored  : 82.23 %
  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: -0.92 (0.28), residues: 900
  helix:  1.03 (0.27), residues: 402
  sheet: -2.39 (0.32), residues: 186
  loop : -1.51 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.020   0.001   PHE R  39 
 TYR   0.008   0.001   TYR R 221 
 ARG   0.006   0.000   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  306 GLN cc_start: 0.7510 (tp40) cc_final: 0.7241 (tp40)
REVERT: B  129 ARG cc_start: 0.7121 (tpt90) cc_final: 0.5978 (mtp-110)
REVERT: B  163 ASP cc_start: 0.7184 (t0) cc_final: 0.6778 (t0)
REVERT: B  200 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (m)
REVERT: B  214 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6830 (mmt180)
REVERT: B  226 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: B  234 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8439 (m-80)
REVERT: B  258 ASP cc_start: 0.6521 (t70) cc_final: 0.5760 (t70)
REVERT: R  113 MET cc_start: 0.6651 (ttp) cc_final: 0.6416 (tmm)
REVERT: R  323 MET cc_start: 0.6539 (mmm) cc_final: 0.5777 (mtt)
  outliers start: 21
  outliers final: 15
  residues processed: 108
  average time/residue: 0.2206
  time to fit residues: 31.0326
Evaluate side-chains
  100 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   92 ASP
Chi-restraints excluded: chain R residue  207 THR
Chi-restraints excluded: chain R residue  253 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.187232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.137038 restraints weight = 7650.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.42
r_work: 0.3388 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7319  Z= 0.160
  Angle     :  0.469   5.328   9912  Z= 0.246
  Chirality :  0.040   0.153   1135
  Planarity :  0.003   0.038   1247
  Dihedral  :  4.141  47.326    994
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.81 %
    Favored  : 78.86 %
  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: -0.54 (0.28), residues: 900
  helix:  1.25 (0.27), residues: 408
  sheet: -2.06 (0.34), residues: 180
  loop : -1.36 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 261 
 HIS   0.002   0.001   HIS L   7 
 PHE   0.016   0.001   PHE R  39 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.005   0.000   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.6888 (ttp80) cc_final: 0.6613 (ttp-110)
REVERT: B  129 ARG cc_start: 0.7111 (tpt90) cc_final: 0.6004 (mtp-110)
REVERT: B  163 ASP cc_start: 0.7283 (t0) cc_final: 0.6949 (t0)
REVERT: B  200 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8114 (m)
REVERT: B  214 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6859 (mmt180)
REVERT: B  226 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: B  234 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8399 (m-80)
REVERT: B  258 ASP cc_start: 0.6409 (t70) cc_final: 0.5672 (t70)
REVERT: R   91 ARG cc_start: 0.3651 (OUTLIER) cc_final: 0.3160 (ptp-170)
REVERT: R  323 MET cc_start: 0.6490 (mmm) cc_final: 0.5657 (mtt)
  outliers start: 18
  outliers final: 13
  residues processed: 99
  average time/residue: 0.2352
  time to fit residues: 30.3931
Evaluate side-chains
  101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.187039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137056 restraints weight = 7630.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.36
r_work: 0.3384 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7319  Z= 0.160
  Angle     :  0.470   9.007   9912  Z= 0.242
  Chirality :  0.040   0.139   1135
  Planarity :  0.003   0.038   1247
  Dihedral  :  3.761  17.755    992
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.90 %
    Favored  : 78.73 %
  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 (0.29), residues: 900
  helix:  1.40 (0.27), residues: 408
  sheet: -1.87 (0.35), residues: 182
  loop : -1.22 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS L   7 
 PHE   0.014   0.001   PHE R  39 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B  52 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.6966 (ttp80) cc_final: 0.6715 (ttp-110)
REVERT: B   17 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: B  129 ARG cc_start: 0.7192 (tpt90) cc_final: 0.6048 (mtp-110)
REVERT: B  200 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8105 (m)
REVERT: B  214 ARG cc_start: 0.7859 (mtt180) cc_final: 0.6793 (mmt180)
REVERT: B  217 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7647 (mtm)
REVERT: B  226 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8506 (mt-10)
REVERT: B  234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (m-80)
REVERT: B  258 ASP cc_start: 0.6589 (t70) cc_final: 0.5842 (t70)
REVERT: R   91 ARG cc_start: 0.3593 (OUTLIER) cc_final: 0.3072 (ptp-170)
REVERT: R  120 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4786 (tt)
REVERT: R  183 MET cc_start: 0.7314 (mtp) cc_final: 0.7076 (ttm)
REVERT: R  187 MET cc_start: 0.3822 (mmm) cc_final: 0.3496 (ttm)
REVERT: R  323 MET cc_start: 0.6444 (mmm) cc_final: 0.5625 (mtt)
  outliers start: 26
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2278
  time to fit residues: 32.2140
Evaluate side-chains
  103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  207 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 48 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.186714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136512 restraints weight = 7578.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.35
r_work: 0.3377 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7319  Z= 0.194
  Angle     :  0.480   8.700   9912  Z= 0.248
  Chirality :  0.040   0.138   1135
  Planarity :  0.003   0.047   1247
  Dihedral  :  3.801  19.765    992
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.97 %
    Favored  : 77.56 %
  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 (0.29), residues: 900
  helix:  1.43 (0.27), residues: 408
  sheet: -1.78 (0.35), residues: 182
  loop : -1.16 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 261 
 HIS   0.003   0.001   HIS L   7 
 PHE   0.013   0.001   PHE R  39 
 TYR   0.007   0.001   TYR B 264 
 ARG   0.004   0.000   ARG B  52 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.768 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: B  129 ARG cc_start: 0.7159 (tpt90) cc_final: 0.6108 (mtp-110)
REVERT: B  200 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8127 (m)
REVERT: B  214 ARG cc_start: 0.7848 (mtt180) cc_final: 0.6776 (mmt180)
REVERT: B  217 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7581 (mtm)
REVERT: B  226 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8439 (mt-10)
REVERT: B  234 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8332 (m-80)
REVERT: B  258 ASP cc_start: 0.6666 (t70) cc_final: 0.5863 (t70)
REVERT: R   91 ARG cc_start: 0.3670 (OUTLIER) cc_final: 0.3160 (ptp-170)
REVERT: R  183 MET cc_start: 0.7339 (mtp) cc_final: 0.7009 (ttm)
REVERT: R  187 MET cc_start: 0.3830 (mmm) cc_final: 0.3527 (ttm)
REVERT: R  323 MET cc_start: 0.6413 (mmm) cc_final: 0.5558 (mtt)
  outliers start: 19
  outliers final: 14
  residues processed: 97
  average time/residue: 0.2361
  time to fit residues: 29.6225
Evaluate side-chains
  99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  207 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.187694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137348 restraints weight = 7534.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.35
r_work: 0.3390 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7319  Z= 0.160
  Angle     :  0.462   8.079   9912  Z= 0.238
  Chirality :  0.040   0.138   1135
  Planarity :  0.003   0.040   1247
  Dihedral  :  3.667  17.345    992
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.84 %
    Favored  : 77.43 %
  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: -0.07 (0.29), residues: 900
  helix:  1.54 (0.27), residues: 408
  sheet: -1.73 (0.35), residues: 186
  loop : -1.01 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 261 
 HIS   0.003   0.001   HIS L   7 
 PHE   0.012   0.001   PHE R  39 
 TYR   0.007   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  52 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.863 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: B  129 ARG cc_start: 0.7118 (tpt90) cc_final: 0.6044 (mtp-110)
REVERT: B  200 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8066 (m)
REVERT: B  217 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7564 (mtm)
REVERT: B  226 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8404 (mt-10)
REVERT: B  234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8353 (m-80)
REVERT: B  258 ASP cc_start: 0.6602 (t70) cc_final: 0.5774 (t70)
REVERT: R   91 ARG cc_start: 0.3540 (OUTLIER) cc_final: 0.3070 (ptp-170)
REVERT: R  120 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4682 (tt)
REVERT: R  183 MET cc_start: 0.7300 (mtp) cc_final: 0.7007 (ttm)
REVERT: R  187 MET cc_start: 0.3725 (mmm) cc_final: 0.3460 (ttm)
REVERT: R  323 MET cc_start: 0.6502 (mmm) cc_final: 0.5577 (mtt)
  outliers start: 21
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2220
  time to fit residues: 30.0827
Evaluate side-chains
  105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  207 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0570
   chunk 41 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.188650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138295 restraints weight = 7606.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.35
r_work: 0.3399 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7319  Z= 0.145
  Angle     :  0.454   7.740   9912  Z= 0.233
  Chirality :  0.039   0.138   1135
  Planarity :  0.003   0.041   1247
  Dihedral  :  3.595  16.301    992
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.36 %
    Favored  : 77.43 %
  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:  0.09 (0.29), residues: 900
  helix:  1.64 (0.27), residues: 407
  sheet: -1.60 (0.36), residues: 186
  loop : -0.92 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS L   7 
 PHE   0.011   0.001   PHE R  39 
 TYR   0.006   0.001   TYR B  59 
 ARG   0.006   0.000   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7091 (tm-30)
REVERT: B  129 ARG cc_start: 0.7091 (tpt90) cc_final: 0.6035 (mtp-110)
REVERT: B  200 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8071 (m)
REVERT: B  217 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7509 (mtm)
REVERT: B  226 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8378 (mt-10)
REVERT: B  234 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8376 (m-80)
REVERT: B  258 ASP cc_start: 0.6546 (t70) cc_final: 0.5704 (t70)
REVERT: R   91 ARG cc_start: 0.3580 (OUTLIER) cc_final: 0.3109 (ptp-170)
REVERT: R  120 LEU cc_start: 0.5118 (OUTLIER) cc_final: 0.4645 (tt)
REVERT: R  183 MET cc_start: 0.7230 (mtp) cc_final: 0.6958 (ttm)
REVERT: R  187 MET cc_start: 0.3436 (mmm) cc_final: 0.3152 (ttm)
REVERT: R  309 TYR cc_start: 0.7592 (m-80) cc_final: 0.7348 (m-80)
REVERT: R  323 MET cc_start: 0.6578 (mmm) cc_final: 0.5668 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 101
  average time/residue: 0.2239
  time to fit residues: 29.7478
Evaluate side-chains
  106 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  120 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.185412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.134842 restraints weight = 7678.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.35
r_work: 0.3367 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7319  Z= 0.240
  Angle     :  0.499   8.464   9912  Z= 0.258
  Chirality :  0.041   0.137   1135
  Planarity :  0.004   0.045   1247
  Dihedral  :  3.829  19.240    992
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.62 %
    Favored  : 76.78 %
  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: -0.04 (0.29), residues: 900
  helix:  1.55 (0.27), residues: 408
  sheet: -1.73 (0.36), residues: 187
  loop : -0.94 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 261 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.013   0.001   PHE R  78 
 TYR   0.014   0.001   TYR A 287 
 ARG   0.006   0.000   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  277 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8294 (ttmt)
REVERT: B   17 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: B  129 ARG cc_start: 0.7109 (tpt90) cc_final: 0.6034 (mtp-110)
REVERT: B  163 ASP cc_start: 0.7646 (t0) cc_final: 0.7419 (t0)
REVERT: B  200 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (m)
REVERT: B  214 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6759 (mmt180)
REVERT: B  217 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7473 (mtm)
REVERT: B  226 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8389 (mt-10)
REVERT: B  234 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8256 (m-80)
REVERT: R   91 ARG cc_start: 0.3636 (OUTLIER) cc_final: 0.3159 (ptp-170)
REVERT: R  120 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4861 (tt)
REVERT: R  183 MET cc_start: 0.7270 (mtp) cc_final: 0.7000 (ttm)
REVERT: R  187 MET cc_start: 0.3548 (mmm) cc_final: 0.3289 (ttm)
REVERT: R  242 LYS cc_start: 0.8112 (mmtt) cc_final: 0.6759 (mtmt)
REVERT: R  309 TYR cc_start: 0.7676 (m-80) cc_final: 0.7345 (m-80)
REVERT: R  323 MET cc_start: 0.6553 (mmm) cc_final: 0.5641 (mtt)
  outliers start: 20
  outliers final: 14
  residues processed: 99
  average time/residue: 0.2236
  time to fit residues: 29.0273
Evaluate side-chains
  106 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  207 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0670
   chunk 69 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.188344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.138032 restraints weight = 7744.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.40
r_work: 0.3394 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7319  Z= 0.142
  Angle     :  0.458   7.502   9912  Z= 0.236
  Chirality :  0.040   0.142   1135
  Planarity :  0.003   0.039   1247
  Dihedral  :  3.621  17.391    992
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.66 %
    Favored  : 76.52 %
  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 (0.30), residues: 900
  helix:  1.73 (0.27), residues: 404
  sheet: -1.53 (0.37), residues: 186
  loop : -0.78 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 261 
 HIS   0.002   0.001   HIS L   7 
 PHE   0.011   0.001   PHE R  39 
 TYR   0.010   0.001   TYR A 287 
 ARG   0.007   0.000   ARG G  62 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  277 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8280 (ttmt)
REVERT: B   17 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7101 (tm-30)
REVERT: B  129 ARG cc_start: 0.7074 (tpt90) cc_final: 0.6021 (mtp-110)
REVERT: B  200 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8060 (m)
REVERT: B  217 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7535 (mtm)
REVERT: B  226 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8407 (mt-10)
REVERT: B  234 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8360 (m-80)
REVERT: B  258 ASP cc_start: 0.6519 (t70) cc_final: 0.5684 (t70)
REVERT: G   21 MET cc_start: 0.8008 (tmm) cc_final: 0.7742 (tmm)
REVERT: G   58 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: R   91 ARG cc_start: 0.3315 (OUTLIER) cc_final: 0.2797 (ptp-170)
REVERT: R  120 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4540 (tt)
REVERT: R  183 MET cc_start: 0.7272 (mtp) cc_final: 0.7013 (ttm)
REVERT: R  242 LYS cc_start: 0.8143 (mmtt) cc_final: 0.6829 (mtmt)
REVERT: R  309 TYR cc_start: 0.7589 (m-80) cc_final: 0.7296 (m-80)
REVERT: R  323 MET cc_start: 0.6567 (mmm) cc_final: 0.5654 (mtt)
  outliers start: 14
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2332
  time to fit residues: 30.6730
Evaluate side-chains
  104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue   91 ARG
Chi-restraints excluded: chain R residue  120 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.183483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132414 restraints weight = 7628.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.54
r_work: 0.3324 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7319  Z= 0.279
  Angle     :  0.521   8.690   9912  Z= 0.270
  Chirality :  0.042   0.139   1135
  Planarity :  0.004   0.045   1247
  Dihedral  :  3.936  20.187    992
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.75 %
    Favored  : 76.78 %
  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: -0.02 (0.29), residues: 900
  helix:  1.52 (0.27), residues: 408
  sheet: -1.66 (0.35), residues: 193
  loop : -0.89 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 261 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.013   0.001   PHE R  78 
 TYR   0.014   0.001   TYR R 221 
 ARG   0.007   0.000   ARG G  62 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4171.78 seconds
wall clock time: 72 minutes 15.64 seconds (4335.64 seconds total)