Starting phenix.real_space_refine
on Thu Mar 13 17:58:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zfz_60072/03_2025/8zfz_60072.cif"
  }
  resolution = 3.3
  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=  -0.002 sd=   0.058
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      59      5.16       5
     C    5763      2.51       5
     N    1564      2.21       5
     O    1679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 9065
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2576
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          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: "D"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1756
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1932
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          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: 2377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2377
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 287}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
  Time building chain proxies: 5.19, per 1000 atoms: 0.57
  Number of scatterers: 9065
  At special positions: 0
  Unit cell: (89.28, 115.32, 130.2, 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      59     16.00
     O    1679      8.00
     N    1564      7.00
     C    5763      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 134 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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: 2.07
  Conformation dependent library (CDL) restraints added in 993.9 milliseconds
  

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2154

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      37.4% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 15
    Processing helix  chain 'B' and resid 15 through 25
      removed outlier: 3.761A  pdb=" N   ARG B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LYS B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.677A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 258 through 262
      removed outlier: 4.096A  pdb=" N   VAL D 262 " --> pdb=" O   ALA D 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.531A  pdb=" N   GLN A 229 " --> pdb=" O   LYS A 226 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASN A 232 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 261
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 3.904A  pdb=" N   ARG A 266 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 4.320A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 333
      removed outlier: 3.854A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 374
    Processing helix  chain 'R' and resid 23 through 56
      removed outlier: 4.039A  pdb=" N   GLN R  28 " --> pdb=" O   ASP R  24 " (cutoff:3.500A)
      Proline residue:  R  29  - end of helix
      removed outlier: 3.787A  pdb=" N   ILE R  33 " --> pdb=" O   PRO R  29 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ILE R  34 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      Proline residue:  R  41  - end of helix
    Processing helix  chain 'R' and resid 59 through 78
      removed outlier: 3.991A  pdb=" N   LEU R  67 " --> pdb=" O   TYR R  63 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR R  74 " --> pdb=" O   ALA R  70 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 86
      removed outlier: 4.117A  pdb=" N   ASP R  83 " --> pdb=" O   PRO R  79 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 95 through 128
      removed outlier: 4.521A  pdb=" N   PHE R 101 " --> pdb=" O   SER R  97 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLY R 102 " --> pdb=" O   CYS R  98 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ILE R 109 " --> pdb=" O   PHE R 105 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   TYR R 110 " --> pdb=" O   TYR R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 157
    Processing helix  chain 'R' and resid 159 through 164
      removed outlier: 3.664A  pdb=" N   HIS R 163 " --> pdb=" O   ALA R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 219
      removed outlier: 5.731A  pdb=" N   ALA R 200 " --> pdb=" O   LEU R 196 " (cutoff:3.500A)
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 223 through 259
      Proline residue:  R 247  - end of helix
    Processing helix  chain 'R' and resid 269 through 295
      removed outlier: 3.926A  pdb=" N   GLY R 274 " --> pdb=" O   GLU R 270 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA R 275 " --> pdb=" O   ASN R 271 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU R 285 " --> pdb=" O   ALA R 281 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASN R 286 " --> pdb=" O   LEU R 282 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   CYS R 287 " --> pdb=" O   THR R 283 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   VAL R 288 " --> pdb=" O   SER R 284 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing helix  chain 'R' and resid 298 through 314
    Processing helix  chain 'G' and resid 9 through 23
    Processing helix  chain 'G' and resid 30 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.374A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.130A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.058A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 160
      removed outlier: 7.040A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.543A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.356A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.814A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 45
    Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 50
      removed outlier: 3.709A  pdb=" N   VAL D 135 " --> pdb=" O   HIS D  73 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   MET D  72 " --> pdb=" O   TYR D  88 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   TYR D  88 " --> pdb=" O   MET D  72 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   TRP D  74 " --> pdb=" O   VAL D  86 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 197
    Processing sheet with id=AB2, first strand: chain 'D' and resid 213 through 217
    Processing sheet with id=AB3, first strand: chain 'A' and resid 203 through 207
      removed outlier: 5.997A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   PHE A 239 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ASN A 275 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A 241 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1164 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: 2.38

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2959
        1.34 -     1.46: 2277
        1.46 -     1.58: 3946
        1.58 -     1.70: 1
        1.70 -     1.82: 84
  Bond restraints: 9267
  Sorted by residual:
  bond pdb=" CB  PRO A 344 "
       pdb=" CG  PRO A 344 "
    ideal  model  delta    sigma   weight residual
    1.492  1.633 -0.141 5.00e-02 4.00e+02 7.93e+00
  bond pdb=" CB  LYS G  46 "
       pdb=" CG  LYS G  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.570 -0.050 3.00e-02 1.11e+03 2.83e+00
  bond pdb=" CG  PRO A 344 "
       pdb=" CD  PRO A 344 "
    ideal  model  delta    sigma   weight residual
    1.503  1.551 -0.048 3.40e-02 8.65e+02 2.03e+00
  bond pdb=" CB  ASP A  26 "
       pdb=" CG  ASP A  26 "
    ideal  model  delta    sigma   weight residual
    1.516  1.485  0.031 2.50e-02 1.60e+03 1.53e+00
  bond pdb=" CB  CYS B 149 "
       pdb=" SG  CYS B 149 "
    ideal  model  delta    sigma   weight residual
    1.808  1.769  0.039 3.30e-02 9.18e+02 1.43e+00
  ... (remaining 9262 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 12298
        2.13 -     4.25: 222
        4.25 -     6.38: 33
        6.38 -     8.50: 9
        8.50 -    10.63: 4
  Bond angle restraints: 12566
  Sorted by residual:
  angle pdb=" CA  PRO A 344 "
        pdb=" N   PRO A 344 "
        pdb=" CD  PRO A 344 "
      ideal   model   delta    sigma   weight residual
     112.00  103.02    8.98 1.40e+00 5.10e-01 4.11e+01
  angle pdb=" CA  LYS G  46 "
        pdb=" CB  LYS G  46 "
        pdb=" CG  LYS G  46 "
      ideal   model   delta    sigma   weight residual
     114.10  122.03   -7.93 2.00e+00 2.50e-01 1.57e+01
  angle pdb=" CB  MET D 131 "
        pdb=" CG  MET D 131 "
        pdb=" SD  MET D 131 "
      ideal   model   delta    sigma   weight residual
     112.70  123.33  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" CB  LYS G  46 "
        pdb=" CG  LYS G  46 "
        pdb=" CD  LYS G  46 "
      ideal   model   delta    sigma   weight residual
     111.30  119.40   -8.10 2.30e+00 1.89e-01 1.24e+01
  angle pdb=" CA  MET G  21 "
        pdb=" CB  MET G  21 "
        pdb=" CG  MET G  21 "
      ideal   model   delta    sigma   weight residual
     114.10  120.86   -6.76 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 12561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4527
       17.52 -    35.05: 702
       35.05 -    52.57: 193
       52.57 -    70.10: 37
       70.10 -    87.62: 15
  Dihedral angle restraints: 5474
    sinusoidal: 2126
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" CB  CYS D  60 "
           pdb=" SG  CYS D  60 "
           pdb=" SG  CYS D 134 "
           pdb=" CB  CYS D 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   24.70   68.30     1      1.00e+01 1.00e-02 6.05e+01
  dihedral pdb=" CB  CYS R  98 "
           pdb=" SG  CYS R  98 "
           pdb=" SG  CYS R 176 "
           pdb=" CB  CYS R 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.56   53.56     1      1.00e+01 1.00e-02 3.90e+01
  dihedral pdb=" CA  TRP D  85 "
           pdb=" C   TRP D  85 "
           pdb=" N   VAL D  86 "
           pdb=" CA  VAL D  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.04   28.96     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 5471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 991
       0.042 -    0.084: 305
       0.084 -    0.126: 95
       0.126 -    0.168: 9
       0.168 -    0.211: 3
  Chirality restraints: 1403
  Sorted by residual:
  chirality pdb=" CA  PRO A 344 "
            pdb=" N   PRO A 344 "
            pdb=" C   PRO A 344 "
            pdb=" CB  PRO A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CG  LEU R 131 "
            pdb=" CB  LEU R 131 "
            pdb=" CD1 LEU R 131 "
            pdb=" CD2 LEU R 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CG  LEU R 280 "
            pdb=" CB  LEU R 280 "
            pdb=" CD1 LEU R 280 "
            pdb=" CD2 LEU R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 8.70e-01
  ... (remaining 1400 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  85 "   -0.018 2.00e-02 2.50e+03   2.15e-02 1.16e+01
        pdb=" CG  TRP D  85 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  85 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  85 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  85 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  85 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  85 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  85 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  85 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  85 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 343 "    0.045 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO A 344 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 344 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 344 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R  48 "   -0.019 2.00e-02 2.50e+03   1.53e-02 5.85e+00
        pdb=" CG  TRP R  48 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP R  48 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP R  48 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R  48 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R  48 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R  48 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R  48 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R  48 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R  48 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 388
        2.71 -     3.25: 9694
        3.25 -     3.80: 15798
        3.80 -     4.35: 19422
        4.35 -     4.90: 31889
  Nonbonded interactions: 77191
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OD2 ASP B 170 "
            pdb=" OG1 THR B 173 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASP B 170 "
            pdb=" OG1 THR B 177 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.214 3.040
  ... (remaining 77186 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:             1.090
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.780
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141   9267  Z= 0.256
  Angle     :  0.720  10.628  12566  Z= 0.375
  Chirality :  0.045   0.211   1403
  Planarity :  0.005   0.064   1604
  Dihedral  : 18.502  87.623   3314
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 20.94
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.36 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 40.62 %
    Favored  : 58.67 %
  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: -1.00 (0.25), residues: 1141
  helix:  0.56 (0.27), residues: 386
  sheet: -0.76 (0.35), residues: 237
  loop : -1.54 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.003   TRP D  85 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.025   0.002   PHE R 177 
 TYR   0.014   0.002   TYR R  84 
 ARG   0.006   0.001   ARG R 217 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 173
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7344 (tpt170)
REVERT: B  207 SER cc_start: 0.7893 (m) cc_final: 0.7454 (p)
REVERT: B  325 MET cc_start: 0.7810 (ttt) cc_final: 0.7318 (ttp)
REVERT: D  125 ARG cc_start: 0.7072 (mtm180) cc_final: 0.6571 (ptt-90)
REVERT: D  217 GLN cc_start: 0.6163 (tt0) cc_final: 0.5870 (tt0)
REVERT: A  261 ASN cc_start: 0.7855 (m-40) cc_final: 0.7644 (m-40)
REVERT: A  323 PHE cc_start: 0.7234 (t80) cc_final: 0.6893 (t80)
REVERT: R  248 TYR cc_start: 0.7406 (t80) cc_final: 0.6837 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 178
  average time/residue: 0.2261
  time to fit residues: 54.6678
Evaluate side-chains
  161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0870
   chunk 65 optimal weight:    8.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  43 ASN
A 250 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.219304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.178748 restraints weight = 10582.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 2.78
r_work: 0.3934 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9267  Z= 0.209
  Angle     :  0.619   6.647  12566  Z= 0.323
  Chirality :  0.043   0.158   1403
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.173  38.029   1266
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.75 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 33.13 %
    Favored  : 60.10 %
  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: -1.00 (0.25), residues: 1141
  helix:  0.64 (0.27), residues: 385
  sheet: -0.77 (0.34), residues: 237
  loop : -1.60 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  85 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.014   0.001   PHE R 177 
 TYR   0.022   0.001   TYR B 145 
 ARG   0.004   0.000   ARG B 314 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 159
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6827 (tpp-160)
REVERT: B  207 SER cc_start: 0.8154 (m) cc_final: 0.7906 (p)
REVERT: B  234 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7178 (m-80)
REVERT: D  125 ARG cc_start: 0.6664 (mtm180) cc_final: 0.6300 (ptt-90)
REVERT: A  250 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7323 (tp40)
REVERT: R  248 TYR cc_start: 0.7477 (t80) cc_final: 0.6942 (t80)
  outliers start: 66
  outliers final: 37
  residues processed: 213
  average time/residue: 0.2079
  time to fit residues: 61.8798
Evaluate side-chains
  187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 148
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain A residue   28 GLN
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   91 TRP
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0570
   chunk 107 optimal weight:    8.9990
   chunk 16 optimal weight:    0.4980
   chunk 21 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.221712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.181591 restraints weight = 10904.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 2.88
r_work: 0.3919 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9267  Z= 0.205
  Angle     :  0.603   8.183  12566  Z= 0.312
  Chirality :  0.043   0.162   1403
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.077  37.488   1264
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.57 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 31.28 %
    Favored  : 61.13 %
  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: -0.87 (0.25), residues: 1141
  helix:  0.76 (0.27), residues: 387
  sheet: -0.68 (0.35), residues: 223
  loop : -1.54 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  85 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.016   0.001   PHE R 177 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.004   0.000   ARG B 256 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 157
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  207 SER cc_start: 0.8174 (m) cc_final: 0.7941 (p)
REVERT: B  234 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7062 (m-80)
REVERT: B  325 MET cc_start: 0.7566 (ttt) cc_final: 0.7356 (ttp)
REVERT: A  340 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6529 (p90)
REVERT: R   45 MET cc_start: 0.6037 (mtt) cc_final: 0.5580 (tpt)
REVERT: R  151 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5411 (mt)
REVERT: R  223 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5559 (pm20)
REVERT: R  248 TYR cc_start: 0.7534 (t80) cc_final: 0.7042 (t80)
  outliers start: 74
  outliers final: 49
  residues processed: 216
  average time/residue: 0.2005
  time to fit residues: 60.6332
Evaluate side-chains
  203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 150
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  340 HIS
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  223 GLU
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  277 HIS
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0370
   chunk 2 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.221885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.180604 restraints weight = 10807.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 2.68
r_work: 0.3957 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9267  Z= 0.182
  Angle     :  0.592   6.949  12566  Z= 0.305
  Chirality :  0.042   0.162   1403
  Planarity :  0.004   0.042   1604
  Dihedral  :  4.982  36.591   1264
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.75 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 31.49 %
    Favored  : 61.13 %
  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: -0.82 (0.25), residues: 1141
  helix:  0.89 (0.27), residues: 387
  sheet: -0.75 (0.34), residues: 241
  loop : -1.55 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  63 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.016   0.001   PHE R 177 
 TYR   0.018   0.001   TYR R  84 
 ARG   0.004   0.000   ARG B 256 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 161
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.6446 (mp0) cc_final: 0.6235 (mp0)
REVERT: B  234 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7013 (m-80)
REVERT: B  256 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (tmt-80)
REVERT: D  217 GLN cc_start: 0.7249 (tt0) cc_final: 0.6817 (tt0)
REVERT: A  261 ASN cc_start: 0.7121 (m110) cc_final: 0.6920 (m-40)
REVERT: A  340 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6481 (p90)
REVERT: R   45 MET cc_start: 0.6123 (mtt) cc_final: 0.5598 (tpt)
REVERT: R   84 TYR cc_start: 0.7115 (t80) cc_final: 0.6817 (t80)
REVERT: R  151 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.5397 (mt)
REVERT: R  176 CYS cc_start: 0.4877 (OUTLIER) cc_final: 0.4666 (m)
REVERT: R  194 THR cc_start: 0.6173 (OUTLIER) cc_final: 0.5848 (m)
REVERT: R  248 TYR cc_start: 0.7530 (t80) cc_final: 0.6965 (t80)
  outliers start: 72
  outliers final: 51
  residues processed: 216
  average time/residue: 0.2015
  time to fit residues: 60.7117
Evaluate side-chains
  208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 151
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  204 CYS
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 B residue  256 ARG
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   28 GLN
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  340 HIS
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   91 TRP
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  277 HIS
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain G residue   48 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 104 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.210991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.169313 restraints weight = 11037.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 3.38
r_work: 0.3738 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   9267  Z= 0.489
  Angle     :  0.747   7.151  12566  Z= 0.391
  Chirality :  0.048   0.190   1403
  Planarity :  0.005   0.044   1604
  Dihedral  :  5.533  34.212   1263
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.24 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  9.85 %
    Allowed  : 29.54 %
    Favored  : 60.62 %
  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: -1.25 (0.24), residues: 1141
  helix:  0.33 (0.26), residues: 386
  sheet: -0.94 (0.34), residues: 225
  loop : -1.64 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP B 297 
 HIS   0.005   0.001   HIS R 249 
 PHE   0.023   0.003   PHE R 177 
 TYR   0.033   0.003   TYR D  88 
 ARG   0.008   0.001   ARG A  54 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 155
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7577 (ptpt)
REVERT: B   75 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6849 (pt0)
REVERT: B   89 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6440 (ptpp)
REVERT: B  219 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7466 (mtp-110)
REVERT: B  230 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (t0)
REVERT: B  234 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7077 (m-80)
REVERT: B  256 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7795 (tmt-80)
REVERT: D   84 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5896 (pt0)
REVERT: A   46 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7569 (pttt)
REVERT: A  204 LYS cc_start: 0.5976 (tppt) cc_final: 0.5450 (ttpt)
REVERT: R   45 MET cc_start: 0.6236 (mtt) cc_final: 0.5718 (tpt)
REVERT: R   84 TYR cc_start: 0.7090 (t80) cc_final: 0.6708 (t80)
REVERT: R  176 CYS cc_start: 0.4854 (OUTLIER) cc_final: 0.4579 (m)
REVERT: R  194 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6134 (m)
REVERT: R  248 TYR cc_start: 0.7631 (t80) cc_final: 0.6976 (t80)
  outliers start: 96
  outliers final: 68
  residues processed: 229
  average time/residue: 0.2047
  time to fit residues: 65.9240
Evaluate side-chains
  224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 147
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  155 LEU
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   28 GLN
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  342 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   91 TRP
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 224 GLN
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.218743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.178436 restraints weight = 10906.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 2.74
r_work: 0.3896 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9267  Z= 0.215
  Angle     :  0.625   8.161  12566  Z= 0.324
  Chirality :  0.043   0.200   1403
  Planarity :  0.004   0.046   1604
  Dihedral  :  5.179  31.001   1263
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.75 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  8.51 %
    Allowed  : 29.64 %
    Favored  : 61.85 %
  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: -1.02 (0.25), residues: 1141
  helix:  0.61 (0.26), residues: 386
  sheet: -0.74 (0.35), residues: 221
  loop : -1.61 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 297 
 HIS   0.002   0.001   HIS R 277 
 PHE   0.018   0.002   PHE R 177 
 TYR   0.015   0.001   TYR R  84 
 ARG   0.004   0.000   ARG B 197 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 159
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5923 (mtmm)
REVERT: B  234 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6948 (m-80)
REVERT: D   72 MET cc_start: 0.6706 (mmp) cc_final: 0.6491 (mmp)
REVERT: D  147 ASP cc_start: 0.7486 (m-30) cc_final: 0.7198 (m-30)
REVERT: A   26 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6459 (t0)
REVERT: A  250 GLN cc_start: 0.7729 (tp40) cc_final: 0.7385 (tp-100)
REVERT: A  257 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6077 (tptp)
REVERT: A  261 ASN cc_start: 0.7308 (m110) cc_final: 0.6972 (m-40)
REVERT: A  340 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6691 (p90)
REVERT: R   45 MET cc_start: 0.6103 (mtt) cc_final: 0.5639 (tpt)
REVERT: R   84 TYR cc_start: 0.7130 (t80) cc_final: 0.6795 (t80)
REVERT: R  151 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.5592 (mt)
REVERT: R  176 CYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4555 (m)
REVERT: R  194 THR cc_start: 0.6237 (OUTLIER) cc_final: 0.5880 (m)
REVERT: R  248 TYR cc_start: 0.7533 (t80) cc_final: 0.6858 (t80)
  outliers start: 83
  outliers final: 52
  residues processed: 224
  average time/residue: 0.2047
  time to fit residues: 64.0260
Evaluate side-chains
  210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 150
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  340 HIS
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:   40.0000
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0030
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 224 GLN
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.215702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.175175 restraints weight = 11102.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 3.02
r_work: 0.3829 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9267  Z= 0.279
  Angle     :  0.669   9.920  12566  Z= 0.343
  Chirality :  0.044   0.218   1403
  Planarity :  0.004   0.045   1604
  Dihedral  :  5.217  28.072   1263
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.06 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  8.62 %
    Allowed  : 30.56 %
    Favored  : 60.82 %
  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: -1.09 (0.25), residues: 1141
  helix:  0.57 (0.27), residues: 380
  sheet: -0.84 (0.34), residues: 224
  loop : -1.61 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.019   0.002   PHE R 177 
 TYR   0.016   0.002   TYR D  88 
 ARG   0.003   0.000   ARG A  31 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 151
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6615 (pt0)
REVERT: B  161 SER cc_start: 0.8315 (t) cc_final: 0.8015 (p)
REVERT: B  219 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7499 (mtp-110)
REVERT: B  234 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7045 (m-80)
REVERT: B  261 LEU cc_start: 0.8152 (mt) cc_final: 0.7849 (mt)
REVERT: D   72 MET cc_start: 0.6723 (mmp) cc_final: 0.6446 (mmp)
REVERT: D   84 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5889 (pt0)
REVERT: D  147 ASP cc_start: 0.7552 (m-30) cc_final: 0.7267 (m-30)
REVERT: A  204 LYS cc_start: 0.5969 (tppt) cc_final: 0.5316 (ttpt)
REVERT: A  257 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6055 (tptp)
REVERT: A  261 ASN cc_start: 0.7278 (m110) cc_final: 0.6898 (m-40)
REVERT: A  291 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6315 (mm)
REVERT: R   45 MET cc_start: 0.6081 (mtt) cc_final: 0.5578 (tpt)
REVERT: R   84 TYR cc_start: 0.7091 (t80) cc_final: 0.6761 (t80)
REVERT: R  151 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.5688 (mt)
REVERT: R  176 CYS cc_start: 0.4814 (OUTLIER) cc_final: 0.4393 (m)
REVERT: R  194 THR cc_start: 0.6229 (OUTLIER) cc_final: 0.5867 (m)
REVERT: R  248 TYR cc_start: 0.7592 (t80) cc_final: 0.6831 (t80)
REVERT: G   40 TYR cc_start: 0.8172 (t80) cc_final: 0.7863 (t80)
  outliers start: 84
  outliers final: 64
  residues processed: 215
  average time/residue: 0.2116
  time to fit residues: 63.6423
Evaluate side-chains
  219 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 147
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  224 GLN
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  362 CYS
Chi-restraints excluded: chain A residue  367 GLN
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  269 GLU
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 97 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
D 224 GLN
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.219143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.178436 restraints weight = 11129.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.4177 rms_B_bonded: 3.17
r_work: 0.3865 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9267  Z= 0.210
  Angle     :  0.657   9.283  12566  Z= 0.333
  Chirality :  0.044   0.233   1403
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.108  28.853   1263
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.75 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 30.77 %
    Favored  : 61.23 %
  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: -1.02 (0.25), residues: 1141
  helix:  0.72 (0.27), residues: 380
  sheet: -0.84 (0.34), residues: 240
  loop : -1.64 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.017   0.001   PHE R 177 
 TYR   0.019   0.002   TYR A 301 
 ARG   0.002   0.000   ARG B 256 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 155
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7535 (mtp-110)
REVERT: B  234 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7023 (m-80)
REVERT: B  261 LEU cc_start: 0.8090 (mt) cc_final: 0.7820 (mt)
REVERT: D   72 MET cc_start: 0.6621 (mmp) cc_final: 0.6293 (mmp)
REVERT: D   84 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5956 (pt0)
REVERT: D  147 ASP cc_start: 0.7587 (m-30) cc_final: 0.7327 (m-30)
REVERT: D  269 GLN cc_start: 0.5332 (pm20) cc_final: 0.5008 (pm20)
REVERT: A   26 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6267 (t0)
REVERT: A  257 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5996 (tptp)
REVERT: A  261 ASN cc_start: 0.7216 (m110) cc_final: 0.6826 (m-40)
REVERT: A  291 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6331 (mm)
REVERT: A  340 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6669 (p90)
REVERT: R   45 MET cc_start: 0.6154 (mtt) cc_final: 0.5472 (tpt)
REVERT: R   84 TYR cc_start: 0.7157 (t80) cc_final: 0.6847 (t80)
REVERT: R  151 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.5599 (mt)
REVERT: R  176 CYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4607 (m)
REVERT: R  194 THR cc_start: 0.6127 (OUTLIER) cc_final: 0.5789 (m)
REVERT: R  248 TYR cc_start: 0.7568 (t80) cc_final: 0.6786 (t80)
REVERT: R  270 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5915 (mm-30)
REVERT: G   40 TYR cc_start: 0.8187 (t80) cc_final: 0.7908 (t80)
  outliers start: 78
  outliers final: 55
  residues processed: 216
  average time/residue: 0.2123
  time to fit residues: 63.9655
Evaluate side-chains
  214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 149
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  340 HIS
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  270 GLU
Chi-restraints excluded: chain R residue  285 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0770
   overall best weight:    1.5542

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

Flipped N/Q/H residues before XYZ refinement:
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 224 GLN
** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.214877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.172993 restraints weight = 10968.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.4121 rms_B_bonded: 2.77
r_work: 0.3851 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9267  Z= 0.309
  Angle     :  0.707  11.277  12566  Z= 0.360
  Chirality :  0.045   0.233   1403
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.242  27.914   1263
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.24 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  7.79 %
    Allowed  : 31.38 %
    Favored  : 60.82 %
  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: -1.13 (0.25), residues: 1141
  helix:  0.63 (0.27), residues: 378
  sheet: -1.00 (0.33), residues: 241
  loop : -1.64 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.019   0.002   PHE R 177 
 TYR   0.017   0.002   TYR D  88 
 ARG   0.003   0.000   ARG R 137 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 154
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  161 SER cc_start: 0.8452 (t) cc_final: 0.8164 (p)
REVERT: B  219 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7527 (mtp-110)
REVERT: B  220 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7671 (mt0)
REVERT: B  234 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.6915 (m-80)
REVERT: B  261 LEU cc_start: 0.8137 (mt) cc_final: 0.7879 (mt)
REVERT: D   72 MET cc_start: 0.6807 (mmp) cc_final: 0.6456 (mmp)
REVERT: D   84 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5868 (pt0)
REVERT: D  147 ASP cc_start: 0.7501 (m-30) cc_final: 0.7224 (m-30)
REVERT: A  204 LYS cc_start: 0.6109 (tppt) cc_final: 0.5460 (ttpt)
REVERT: A  250 GLN cc_start: 0.7640 (tp40) cc_final: 0.7419 (tp-100)
REVERT: A  257 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6109 (tptp)
REVERT: A  261 ASN cc_start: 0.7299 (m110) cc_final: 0.7054 (m-40)
REVERT: A  291 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6515 (mm)
REVERT: R   45 MET cc_start: 0.6076 (mtt) cc_final: 0.5445 (tpt)
REVERT: R   84 TYR cc_start: 0.7096 (t80) cc_final: 0.6844 (t80)
REVERT: R  151 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.5751 (mt)
REVERT: R  176 CYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4865 (m)
REVERT: R  194 THR cc_start: 0.6192 (OUTLIER) cc_final: 0.5836 (m)
REVERT: R  248 TYR cc_start: 0.7631 (t80) cc_final: 0.6907 (t80)
REVERT: R  270 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.5932 (mm-30)
REVERT: G   40 TYR cc_start: 0.8167 (t80) cc_final: 0.7894 (t80)
  outliers start: 76
  outliers final: 56
  residues processed: 213
  average time/residue: 0.2211
  time to fit residues: 65.4719
Evaluate side-chains
  214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 149
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  297 TRP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  367 GLN
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  269 GLU
Chi-restraints excluded: chain R residue  270 GLU
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0030
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0270
   chunk 47 optimal weight:    7.9990
   overall best weight:    0.4248

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

Flipped N/Q/H residues before XYZ refinement:
D 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.222120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180626 restraints weight = 11098.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 2.74
r_work: 0.3964 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9267  Z= 0.191
  Angle     :  0.661  11.533  12566  Z= 0.333
  Chirality :  0.044   0.203   1403
  Planarity :  0.004   0.042   1604
  Dihedral  :  4.929  26.300   1261
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.57 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 33.23 %
    Favored  : 60.82 %
  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: -0.88 (0.25), residues: 1141
  helix:  0.88 (0.27), residues: 377
  sheet: -0.78 (0.34), residues: 240
  loop : -1.57 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  63 
 HIS   0.003   0.001   HIS R 249 
 PHE   0.015   0.001   PHE R 177 
 TYR   0.014   0.001   TYR R  84 
 ARG   0.003   0.000   ARG B 314 

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

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

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2282 Ramachandran restraints generated.
    1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 159
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7576 (mtp-110)
REVERT: B  234 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6842 (m-80)
REVERT: D  230 MET cc_start: 0.7568 (mmm) cc_final: 0.7224 (mmm)
REVERT: D  269 GLN cc_start: 0.5227 (pm20) cc_final: 0.4313 (pp30)
REVERT: A  215 PHE cc_start: 0.6111 (m-80) cc_final: 0.5505 (m-80)
REVERT: A  250 GLN cc_start: 0.7566 (tp40) cc_final: 0.7284 (tp-100)
REVERT: A  257 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6026 (tptp)
REVERT: A  261 ASN cc_start: 0.7178 (m110) cc_final: 0.6816 (m-40)
REVERT: A  291 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6465 (mm)
REVERT: A  340 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6628 (p90)
REVERT: R   45 MET cc_start: 0.6027 (mtt) cc_final: 0.5401 (tpt)
REVERT: R   84 TYR cc_start: 0.7106 (t80) cc_final: 0.6794 (t80)
REVERT: R  151 LEU cc_start: 0.6810 (tp) cc_final: 0.5548 (mt)
REVERT: R  176 CYS cc_start: 0.5584 (OUTLIER) cc_final: 0.5250 (m)
REVERT: R  194 THR cc_start: 0.6040 (OUTLIER) cc_final: 0.5747 (m)
REVERT: R  248 TYR cc_start: 0.7551 (t80) cc_final: 0.6789 (t80)
REVERT: R  270 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5901 (mm-30)
  outliers start: 58
  outliers final: 46
  residues processed: 207
  average time/residue: 0.2136
  time to fit residues: 61.3716
Evaluate side-chains
  204 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 151
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  204 CYS
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 B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   65 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  156 THR
Chi-restraints excluded: chain D residue  210 THR
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 GLN
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  340 HIS
Chi-restraints excluded: chain A residue  362 CYS
Chi-restraints excluded: chain R residue   36 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  120 SER
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  163 HIS
Chi-restraints excluded: chain R residue  176 CYS
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  270 GLU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  293 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0670
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0270
   chunk 54 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.2774

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

Flipped N/Q/H residues before XYZ refinement:
R  56 GLN
R 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.224620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.184073 restraints weight = 10984.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 2.72
r_work: 0.4001 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9267  Z= 0.178
  Angle     :  0.669  12.991  12566  Z= 0.335
  Chirality :  0.043   0.188   1403
  Planarity :  0.004   0.042   1604
  Dihedral  :  4.803  25.989   1261
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.10 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 34.15 %
    Favored  : 60.41 %
  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: -0.73 (0.25), residues: 1141
  helix:  1.03 (0.27), residues: 376
  sheet: -0.61 (0.36), residues: 221
  loop : -1.53 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B  63 
 HIS   0.003   0.001   HIS R 249 
 PHE   0.014   0.001   PHE R 177 
 TYR   0.023   0.001   TYR G  40 
 ARG   0.006   0.000   ARG B 314 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5343.94 seconds
wall clock time: 95 minutes 49.40 seconds (5749.40 seconds total)