Starting phenix.real_space_refine
on Sat Jun  7 11:46:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trp_26100/06_2025/7trp_26100.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     Cl      1      4.86       5
     C    5535      2.51       5
     N    1461      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8681
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2079
          Classifications: {'peptide': 267}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 10, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2591
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 423
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 1786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1786
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1768
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 34
          Unusual residues: {'IUE': 1, 'IXO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.63
  Number of scatterers: 8681
  At special positions: 0
  Unit cell: (93.79, 119.52, 123.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      64     16.00
     O    1620      8.00
     N    1461      7.00
     C    5535      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      38.6% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 60
      removed outlier: 3.624A  pdb=" N   ASN R  60 " --> pdb=" O   SER R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 64
    Processing helix  chain 'R' and resid 66 through 84
      removed outlier: 4.384A  pdb=" N   PHE R  70 " --> pdb=" O   VAL R  66 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU R  71 " --> pdb=" O   ASN R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 96
    Processing helix  chain 'R' and resid 102 through 136
    Processing helix  chain 'R' and resid 145 through 175
      Proline residue:  R 166  - end of helix
      removed outlier: 5.184A  pdb=" N   GLN R 172 " --> pdb=" O   ILE R 168 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   PHE R 173 " --> pdb=" O   LEU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 191
      removed outlier: 3.564A  pdb=" N   LEU R 190 " --> pdb=" O   ILE R 187 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 204
    Processing helix  chain 'R' and resid 204 through 223
      removed outlier: 3.906A  pdb=" N   ARG R 223 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 426
      Proline residue:  R 415  - end of helix
      removed outlier: 3.537A  pdb=" N   THR R 424 " --> pdb=" O   VAL R 420 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   PHE R 425 " --> pdb=" O   LEU R 421 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 431 through 448
      removed outlier: 3.798A  pdb=" N   SER R 446 " --> pdb=" O   CYS R 442 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 448 through 454
    Processing helix  chain 'R' and resid 457 through 463
      removed outlier: 3.625A  pdb=" N   LYS R 461 " --> pdb=" O   ASN R 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.573A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.653A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 4.355A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 4.128A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.556A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.628A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.254A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.792A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.812A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 351
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.500A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.700A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.994A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.132A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.783A  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: 7.016A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.611A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.545A  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: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.013A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.013A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.626A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.271A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1275 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: 2.83

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1398
        1.31 -     1.44: 2469
        1.44 -     1.57: 4903
        1.57 -     1.69: 1
        1.69 -     1.82: 94
  Bond restraints: 8865
  Sorted by residual:
  bond pdb=" C10 IXO R 702 "
       pdb=" N11 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.270  1.475 -0.205 2.00e-02 2.50e+03 1.05e+02
  bond pdb=" C10 IXO R 702 "
       pdb=" C14 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.492  1.331  0.161 2.00e-02 2.50e+03 6.50e+01
  bond pdb=" C13 IXO R 702 "
       pdb=" O12 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.439  1.544 -0.105 2.00e-02 2.50e+03 2.74e+01
  bond pdb=" C05 IXO R 702 "
       pdb=" C06 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.450  1.528 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" C07 IXO R 702 "
       pdb=" C08 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.454  1.530 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 8860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 11627
        2.00 -     4.00: 356
        4.00 -     6.00: 41
        6.00 -     8.00: 14
        8.00 -     9.99: 3
  Bond angle restraints: 12041
  Sorted by residual:
  angle pdb=" N   GLY H 209 "
        pdb=" CA  GLY H 209 "
        pdb=" C   GLY H 209 "
      ideal   model   delta    sigma   weight residual
     113.18  121.40   -8.22 2.37e+00 1.78e-01 1.20e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.91   -6.37 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" N   ALA R 165 "
        pdb=" CA  ALA R 165 "
        pdb=" C   ALA R 165 "
      ideal   model   delta    sigma   weight residual
     112.75  117.28   -4.53 1.36e+00 5.41e-01 1.11e+01
  angle pdb=" CA  TRP R 440 "
        pdb=" CB  TRP R 440 "
        pdb=" CG  TRP R 440 "
      ideal   model   delta    sigma   weight residual
     113.60  107.43    6.17 1.90e+00 2.77e-01 1.05e+01
  angle pdb=" N   CYS R 429 "
        pdb=" CA  CYS R 429 "
        pdb=" C   CYS R 429 "
      ideal   model   delta    sigma   weight residual
     111.07  114.38   -3.31 1.07e+00 8.73e-01 9.54e+00
  ... (remaining 12036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4906
       16.99 -    33.98: 270
       33.98 -    50.97: 45
       50.97 -    67.96: 9
       67.96 -    84.95: 4
  Dihedral angle restraints: 5234
    sinusoidal: 1974
      harmonic: 3260
  Sorted by residual:
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE A 196 "
           pdb=" C   PHE A 196 "
           pdb=" N   LYS A 197 "
           pdb=" CA  LYS A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  HIS H  35 "
           pdb=" C   HIS H  35 "
           pdb=" N   TRP H  36 "
           pdb=" CA  TRP H  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1099
       0.064 -    0.127: 225
       0.127 -    0.191: 53
       0.191 -    0.255: 5
       0.255 -    0.318: 3
  Chirality restraints: 1385
  Sorted by residual:
  chirality pdb=" CB  VAL R 444 "
            pdb=" CA  VAL R 444 "
            pdb=" CG1 VAL R 444 "
            pdb=" CG2 VAL R 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" CB  ILE A 184 "
            pdb=" CA  ILE A 184 "
            pdb=" CG1 ILE A 184 "
            pdb=" CG2 ILE A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CB  THR R  90 "
            pdb=" CA  THR R  90 "
            pdb=" OG1 THR R  90 "
            pdb=" CG2 THR R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1382 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   IUE R 701 "    0.035 2.00e-02 2.50e+03   3.45e-02 4.17e+01
        pdb=" C   IUE R 701 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   IUE R 701 "   -0.039 2.00e-02 2.50e+03
        pdb=" C1  IUE R 701 "    0.013 2.00e-02 2.50e+03
        pdb=" C2  IUE R 701 "    0.029 2.00e-02 2.50e+03
        pdb=" C3  IUE R 701 "    0.014 2.00e-02 2.50e+03
        pdb=" C4  IUE R 701 "   -0.012 2.00e-02 2.50e+03
        pdb=" C5  IUE R 701 "    0.036 2.00e-02 2.50e+03
        pdb=" C6  IUE R 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C7  IUE R 701 "   -0.003 2.00e-02 2.50e+03
        pdb=" C9  IUE R 701 "   -0.086 2.00e-02 2.50e+03
        pdb=" N2  IUE R 701 "    0.046 2.00e-02 2.50e+03
        pdb=" S   IUE R 701 "    0.016 2.00e-02 2.50e+03
        pdb="CL   IUE R 701 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 IUE R 701 "   -0.057 2.00e-02 2.50e+03   4.82e-02 2.91e+01
        pdb=" C4  IUE R 701 "   -0.045 2.00e-02 2.50e+03
        pdb=" C9  IUE R 701 "    0.021 2.00e-02 2.50e+03
        pdb=" N1  IUE R 701 "    0.076 2.00e-02 2.50e+03
        pdb=" O1  IUE R 701 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 113 "   -0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   TYR R 113 "    0.065 2.00e-02 2.50e+03
        pdb=" O   TYR R 113 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL R 114 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2315
        2.81 -     3.33: 7729
        3.33 -     3.85: 14628
        3.85 -     4.38: 17643
        4.38 -     4.90: 30339
  Nonbonded interactions: 72654
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 113 "
            pdb=" OH  TYR R 416 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   THR R 433 "
            pdb=" OG  SER R 436 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OH  TYR H 175 "
            pdb=" OE2 GLU A   8 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ASN R  87 "
            pdb=" OG1 THR R  90 "
     model   vdw
     2.329 3.040
  ... (remaining 72649 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:             1.110
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.530
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
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      :  0.006   0.205   8869  Z= 0.277
  Angle     :  0.818   9.994  12049  Z= 0.464
  Chirality :  0.056   0.318   1385
  Planarity :  0.007   0.085   1511
  Dihedral  : 11.233  84.947   3118
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.64 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.43 (0.23), residues: 1106
  helix: -0.02 (0.24), residues: 382
  sheet:  0.22 (0.29), residues: 300
  loop : -0.74 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP R 440 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.035   0.003   PHE R 189 
 TYR   0.029   0.002   TYR R 215 
 ARG   0.006   0.000   ARG H 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13106 (  448)
  hydrogen bonds       : angle       5.89039 ( 1275)
  SS BOND              : bond        0.00455 (    4)
  SS BOND              : angle       1.13729 (    8)
  covalent geometry    : bond        0.00555 ( 8865)
  covalent geometry    : angle       0.81768 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: R  210 ILE cc_start: 0.8052 (mm) cc_final: 0.7814 (mp)
REVERT: R  223 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7722 (ttm110)
REVERT: B  270 ILE cc_start: 0.9015 (pt) cc_final: 0.8768 (tp)
REVERT: H  186 GLN cc_start: 0.8733 (tt0) cc_final: 0.8461 (tt0)
REVERT: H  220 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7958 (mm-30)
REVERT: A  302 TYR cc_start: 0.8938 (t80) cc_final: 0.8697 (t80)
REVERT: A  306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8296 (mp10)
REVERT: A  308 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8352 (mt-10)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 1.6575
  time to fit residues: 283.2271
Evaluate side-chains
  123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
R 117 ASN
R 172 GLN
B 268 ASN
H  39 GLN
A 188 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.104736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.065584 restraints weight = 14574.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.67
r_work: 0.2700 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2573 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8869  Z= 0.192
  Angle     :  0.560   5.622  12049  Z= 0.307
  Chirality :  0.043   0.135   1385
  Planarity :  0.004   0.056   1511
  Dihedral  :  4.908  36.829   1225
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.59 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.96 (0.25), residues: 1106
  helix:  1.60 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 287
  loop : -0.25 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 188 
 PHE   0.015   0.002   PHE R 189 
 TYR   0.016   0.002   TYR R  89 
 ARG   0.005   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  448)
  hydrogen bonds       : angle       4.53484 ( 1275)
  SS BOND              : bond        0.00440 (    4)
  SS BOND              : angle       0.81322 (    8)
  covalent geometry    : bond        0.00430 ( 8865)
  covalent geometry    : angle       0.55986 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.977 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6519 (mtt) cc_final: 0.6319 (mtp)
REVERT: R  127 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8600 (p)
REVERT: B  172 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8252 (tp30)
REVERT: B  217 MET cc_start: 0.8670 (pmm) cc_final: 0.8351 (pmt)
REVERT: B  254 ASP cc_start: 0.8648 (t70) cc_final: 0.8386 (t70)
REVERT: B  266 HIS cc_start: 0.8824 (t-90) cc_final: 0.8569 (t-170)
REVERT: G   15 LEU cc_start: 0.8294 (tt) cc_final: 0.7995 (tm)
REVERT: H  186 GLN cc_start: 0.9205 (tt0) cc_final: 0.8849 (tt0)
REVERT: A  306 GLN cc_start: 0.8959 (mm110) cc_final: 0.8392 (mp10)
REVERT: A  308 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8528 (mt-10)
  outliers start: 18
  outliers final: 6
  residues processed: 139
  average time/residue: 1.6102
  time to fit residues: 235.2773
Evaluate side-chains
  119 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
H 194 ASN
A 188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.066390 restraints weight = 14690.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.68
r_work: 0.2721 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8869  Z= 0.133
  Angle     :  0.536   6.550  12049  Z= 0.290
  Chirality :  0.041   0.135   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.696  24.119   1225
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.63 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.23 (0.25), residues: 1106
  helix:  1.93 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 288
  loop : -0.08 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.015   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.005   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  448)
  hydrogen bonds       : angle       4.46633 ( 1275)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       0.78850 (    8)
  covalent geometry    : bond        0.00287 ( 8865)
  covalent geometry    : angle       0.53608 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 1.062 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6566 (mtt) cc_final: 0.6304 (mtp)
REVERT: R  127 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8639 (p)
REVERT: R  136 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7971 (mttm)
REVERT: R  184 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7217 (mm-40)
REVERT: B  172 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8269 (tp30)
REVERT: B  217 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8388 (pmt)
REVERT: B  254 ASP cc_start: 0.8672 (t70) cc_final: 0.8462 (t70)
REVERT: B  266 HIS cc_start: 0.8847 (t-90) cc_final: 0.8529 (t-170)
REVERT: G   15 LEU cc_start: 0.8360 (tt) cc_final: 0.8066 (tm)
REVERT: H  186 GLN cc_start: 0.9220 (tt0) cc_final: 0.8908 (tt0)
REVERT: A  306 GLN cc_start: 0.8907 (mm110) cc_final: 0.8408 (mp10)
  outliers start: 17
  outliers final: 6
  residues processed: 128
  average time/residue: 1.5382
  time to fit residues: 207.5571
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 GLN
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.105349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066614 restraints weight = 14630.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.67
r_work: 0.2722 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8869  Z= 0.135
  Angle     :  0.536   6.550  12049  Z= 0.290
  Chirality :  0.041   0.135   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.696  24.119   1225
  Min Nonbonded Distance : 1.650

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.78 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.23 (0.25), residues: 1106
  helix:  1.93 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 288
  loop : -0.08 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.015   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.005   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  448)
  hydrogen bonds       : angle       4.46633 ( 1275)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       0.78850 (    8)
  covalent geometry    : bond        0.00289 ( 8865)
  covalent geometry    : angle       0.53613 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.978 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6570 (mtt) cc_final: 0.6300 (mtp)
REVERT: R  127 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (p)
REVERT: R  136 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7975 (mttm)
REVERT: R  184 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7203 (mm-40)
REVERT: B  172 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8266 (tp30)
REVERT: B  217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8391 (pmt)
REVERT: B  254 ASP cc_start: 0.8670 (t70) cc_final: 0.8469 (t70)
REVERT: B  266 HIS cc_start: 0.8836 (t-90) cc_final: 0.8534 (t-170)
REVERT: G   15 LEU cc_start: 0.8339 (tt) cc_final: 0.8047 (tm)
REVERT: H  186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8906 (tt0)
REVERT: A  306 GLN cc_start: 0.8905 (mm110) cc_final: 0.8405 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 116
  average time/residue: 1.5259
  time to fit residues: 186.9998
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 GLN
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    0.0070
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.105359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066641 restraints weight = 14552.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.66
r_work: 0.2723 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8869  Z= 0.135
  Angle     :  0.536   6.550  12049  Z= 0.290
  Chirality :  0.041   0.135   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.696  24.119   1225
  Min Nonbonded Distance : 1.650

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.78 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.23 (0.25), residues: 1106
  helix:  1.93 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 288
  loop : -0.08 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.015   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.005   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  448)
  hydrogen bonds       : angle       4.46633 ( 1275)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       0.78850 (    8)
  covalent geometry    : bond        0.00289 ( 8865)
  covalent geometry    : angle       0.53613 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.011 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6576 (mtt) cc_final: 0.6305 (mtp)
REVERT: R  127 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8630 (p)
REVERT: R  136 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7973 (mttm)
REVERT: R  184 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7206 (mm-40)
REVERT: B  172 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8262 (tp30)
REVERT: B  217 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8394 (pmt)
REVERT: B  254 ASP cc_start: 0.8669 (t70) cc_final: 0.8469 (t70)
REVERT: B  266 HIS cc_start: 0.8838 (t-90) cc_final: 0.8536 (t-170)
REVERT: G   15 LEU cc_start: 0.8341 (tt) cc_final: 0.8050 (tm)
REVERT: H  186 GLN cc_start: 0.9217 (tt0) cc_final: 0.8906 (tt0)
REVERT: A  306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8407 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 116
  average time/residue: 1.5514
  time to fit residues: 189.7876
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 GLN
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0670
   chunk 81 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.3324

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.105361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066511 restraints weight = 14499.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.66
r_work: 0.2723 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8869  Z= 0.135
  Angle     :  0.536   6.550  12049  Z= 0.290
  Chirality :  0.041   0.135   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.696  24.119   1225
  Min Nonbonded Distance : 1.650

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.78 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.23 (0.25), residues: 1106
  helix:  1.93 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 288
  loop : -0.08 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.015   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.005   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  448)
  hydrogen bonds       : angle       4.46633 ( 1275)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       0.78850 (    8)
  covalent geometry    : bond        0.00289 ( 8865)
  covalent geometry    : angle       0.53613 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.061 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6569 (mtt) cc_final: 0.6298 (mtp)
REVERT: R  127 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8631 (p)
REVERT: R  136 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7972 (mttm)
REVERT: R  184 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7204 (mm-40)
REVERT: B  172 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8267 (tp30)
REVERT: B  217 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8388 (pmt)
REVERT: B  254 ASP cc_start: 0.8668 (t70) cc_final: 0.8466 (t70)
REVERT: B  266 HIS cc_start: 0.8836 (t-90) cc_final: 0.8534 (t-170)
REVERT: G   15 LEU cc_start: 0.8338 (tt) cc_final: 0.8046 (tm)
REVERT: H  186 GLN cc_start: 0.9217 (tt0) cc_final: 0.8905 (tt0)
REVERT: A  306 GLN cc_start: 0.8905 (mm110) cc_final: 0.8405 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 116
  average time/residue: 1.9789
  time to fit residues: 244.0021
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 GLN
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.105362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.066617 restraints weight = 14729.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 2.68
r_work: 0.2726 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8869  Z= 0.136
  Angle     :  0.559   8.676  12049  Z= 0.299
  Chirality :  0.042   0.141   1385
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.541  22.598   1225
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.35 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.36 (0.26), residues: 1106
  helix:  2.03 (0.27), residues: 395
  sheet:  0.66 (0.30), residues: 293
  loop :  0.08 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 188 
 PHE   0.020   0.001   PHE R  84 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.011   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  448)
  hydrogen bonds       : angle       4.41686 ( 1275)
  SS BOND              : bond        0.00293 (    4)
  SS BOND              : angle       0.88025 (    8)
  covalent geometry    : bond        0.00299 ( 8865)
  covalent geometry    : angle       0.55920 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.073 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6542 (mtt) cc_final: 0.6305 (mtp)
REVERT: R  111 LEU cc_start: 0.7751 (tp) cc_final: 0.7497 (tm)
REVERT: R  127 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8656 (p)
REVERT: B  172 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8258 (tp30)
REVERT: B  217 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8366 (pmt)
REVERT: B  266 HIS cc_start: 0.8914 (t-90) cc_final: 0.8576 (t-170)
REVERT: G   15 LEU cc_start: 0.8362 (tt) cc_final: 0.8064 (tm)
REVERT: H   43 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8496 (mmtm)
REVERT: H  186 GLN cc_start: 0.9215 (tt0) cc_final: 0.8812 (tt0)
REVERT: A  205 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8242 (mmm160)
REVERT: A  306 GLN cc_start: 0.8915 (mm110) cc_final: 0.8368 (mp10)
  outliers start: 14
  outliers final: 7
  residues processed: 125
  average time/residue: 1.5439
  time to fit residues: 203.4893
Evaluate side-chains
  124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   54 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.106148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.067946 restraints weight = 14762.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.65
r_work: 0.2754 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2625 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8869  Z= 0.115
  Angle     :  0.548   8.959  12049  Z= 0.292
  Chirality :  0.041   0.138   1385
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.408  21.615   1225
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.00 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.38 (0.26), residues: 1106
  helix:  2.07 (0.27), residues: 393
  sheet:  0.65 (0.30), residues: 292
  loop :  0.10 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.042   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.011   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  448)
  hydrogen bonds       : angle       4.33913 ( 1275)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       0.70344 (    8)
  covalent geometry    : bond        0.00251 ( 8865)
  covalent geometry    : angle       0.54817 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.939 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6781 (mmp) cc_final: 0.6572 (mmm)
REVERT: B  172 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: B  217 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8400 (pmt)
REVERT: B  266 HIS cc_start: 0.8923 (t-90) cc_final: 0.8640 (t-170)
REVERT: G   15 LEU cc_start: 0.8355 (tt) cc_final: 0.8081 (tm)
REVERT: G   52 THR cc_start: 0.7894 (p) cc_final: 0.7654 (t)
REVERT: H   43 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8505 (mmtm)
REVERT: H  186 GLN cc_start: 0.9215 (tt0) cc_final: 0.8851 (tt0)
REVERT: A  306 GLN cc_start: 0.8908 (mm110) cc_final: 0.8355 (mp10)
  outliers start: 12
  outliers final: 4
  residues processed: 123
  average time/residue: 1.8819
  time to fit residues: 244.7638
Evaluate side-chains
  117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0470
   chunk 70 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.3882

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.106297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.068107 restraints weight = 14603.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.64
r_work: 0.2756 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8869  Z= 0.115
  Angle     :  0.548   8.959  12049  Z= 0.292
  Chirality :  0.041   0.138   1385
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.408  21.615   1225
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.72 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.38 (0.26), residues: 1106
  helix:  2.07 (0.27), residues: 393
  sheet:  0.65 (0.30), residues: 292
  loop :  0.10 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.042   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.011   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  448)
  hydrogen bonds       : angle       4.33913 ( 1275)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       0.70344 (    8)
  covalent geometry    : bond        0.00251 ( 8865)
  covalent geometry    : angle       0.54817 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 1.107 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6797 (mmp) cc_final: 0.6587 (mmm)
REVERT: B  172 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: B  217 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8399 (pmt)
REVERT: B  266 HIS cc_start: 0.8926 (t-90) cc_final: 0.8639 (t-170)
REVERT: G   15 LEU cc_start: 0.8363 (tt) cc_final: 0.8091 (tm)
REVERT: G   52 THR cc_start: 0.7895 (p) cc_final: 0.7650 (t)
REVERT: H   43 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8496 (mmtm)
REVERT: H  186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8857 (tt0)
REVERT: A  306 GLN cc_start: 0.8902 (mm110) cc_final: 0.8357 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 114
  average time/residue: 1.7186
  time to fit residues: 205.7941
Evaluate side-chains
  116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.106146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.068017 restraints weight = 14594.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.64
r_work: 0.2756 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8869  Z= 0.126
  Angle     :  0.569   9.591  12049  Z= 0.301
  Chirality :  0.041   0.161   1385
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.394  20.911   1225
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.07 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.39 (0.26), residues: 1106
  helix:  2.09 (0.27), residues: 393
  sheet:  0.64 (0.30), residues: 292
  loop :  0.09 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.012   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  448)
  hydrogen bonds       : angle       4.34218 ( 1275)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       0.77408 (    8)
  covalent geometry    : bond        0.00279 ( 8865)
  covalent geometry    : angle       0.56892 (12041)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 1.193 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6766 (mmp) cc_final: 0.6563 (mmm)
REVERT: B  172 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: B  217 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8402 (pmt)
REVERT: B  266 HIS cc_start: 0.8925 (t-90) cc_final: 0.8602 (t-170)
REVERT: G   15 LEU cc_start: 0.8343 (tt) cc_final: 0.8073 (tm)
REVERT: G   52 THR cc_start: 0.7900 (p) cc_final: 0.7657 (t)
REVERT: H   43 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8496 (mmtm)
REVERT: H  186 GLN cc_start: 0.9214 (tt0) cc_final: 0.8958 (tt0)
REVERT: A  306 GLN cc_start: 0.8901 (mm110) cc_final: 0.8354 (mp10)
  outliers start: 10
  outliers final: 5
  residues processed: 117
  average time/residue: 1.6216
  time to fit residues: 200.4625
Evaluate side-chains
  117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.106592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.067986 restraints weight = 14562.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.67
r_work: 0.2754 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8869  Z= 0.126
  Angle     :  0.569   9.590  12049  Z= 0.300
  Chirality :  0.041   0.161   1385
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.394  20.911   1225
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.61 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.39 (0.26), residues: 1106
  helix:  2.09 (0.27), residues: 393
  sheet:  0.64 (0.30), residues: 292
  loop :  0.09 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.011   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  448)
  hydrogen bonds       : angle       4.34218 ( 1275)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       0.77417 (    8)
  covalent geometry    : bond        0.00279 ( 8865)
  covalent geometry    : angle       0.56872 (12041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10302.94 seconds
wall clock time: 178 minutes 38.94 seconds (10718.94 seconds total)