Starting phenix.real_space_refine
on Tue Jan 13 21:45:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iys_35830/01_2026/8iys_35830_neut.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.037 sd=   0.146
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      59      5.16       5
     C    6197      2.51       5
     N    1633      2.21       5
     O    1779      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9671
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2791
          Classifications: {'peptide': 355}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 343}
          Unresolved non-hydrogen bonds: 115
          Unresolved non-hydrogen angles: 140
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 9, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 87
    Chain: "B"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2453
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 8, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 73
    Chain: "E"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1732
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "G"
      Number of atoms: 366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 366
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2274
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 12, 'TRANS': 283}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 47
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'YN9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.37, per 1000 atoms: 0.25
  Number of scatterers: 9671
  At special positions: 0
  Unit cell: (95.04, 123.12, 130.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      59     16.00
     P       2     15.00
     F       1      9.00
     O    1779      8.00
     N    1633      7.00
     C    6197      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 499.5 milliseconds
  

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2390

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 13 sheets defined
      40.9% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 62 through 91
      removed outlier: 4.492A  pdb=" N   LYS A  71 " --> pdb=" O   ARG A  67 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   LEU A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 109
      removed outlier: 3.827A  pdb=" N   LYS A 101 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A 102 " --> pdb=" O   GLU A  98 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS A 103 " --> pdb=" O   HIS A  99 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 131
    Processing helix  chain 'A' and resid 132 through 141
    Processing helix  chain 'A' and resid 142 through 145
    Processing helix  chain 'A' and resid 150 through 156
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 169 through 175
    Processing helix  chain 'A' and resid 206 through 210
      removed outlier: 3.517A  pdb=" N   LYS A 209 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 215
    Processing helix  chain 'A' and resid 240 through 254
      removed outlier: 3.586A  pdb=" N   GLU A 244 " --> pdb=" O   ASN A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 259
      removed outlier: 3.654A  pdb=" N   GLN A 259 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 278
      removed outlier: 3.810A  pdb=" N   MET A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 3.537A  pdb=" N   ASP A 284 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'A' and resid 330 through 354
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 3.905A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.517A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 35 through 67
      removed outlier: 3.620A  pdb=" N   ALA R  40 " --> pdb=" O   ARG R  36 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 90
      removed outlier: 3.542A  pdb=" N   CYS R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 102
    Processing helix  chain 'R' and resid 107 through 146
      removed outlier: 4.704A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 169
    Processing helix  chain 'R' and resid 171 through 176
    Processing helix  chain 'R' and resid 200 through 216
    Processing helix  chain 'R' and resid 216 through 243
    Processing helix  chain 'R' and resid 251 through 291
      removed outlier: 3.515A  pdb=" N   SER R 256 " --> pdb=" O   GLN R 252 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   GLN R 257 " --> pdb=" O   ILE R 253 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   GLN R 258 " --> pdb=" O   ARG R 254 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 299 through 312
      removed outlier: 4.129A  pdb=" N   PHE R 303 " --> pdb=" O   TRP R 299 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE R 304 " --> pdb=" O   PRO R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 322
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190
      removed outlier: 9.091A  pdb=" N   SER A 219 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   MET A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   LEU A 223 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 8.519A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ILE A 220 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   PHE A 266 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 222 " --> pdb=" O   PHE A 266 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ASN A 268 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL A 224 " --> pdb=" O   ASN A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.512A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.689A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.159A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.521A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.558A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.668A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.536A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.183A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.766A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 143
    Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149
      removed outlier: 3.839A  pdb=" N   GLU E 247 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU E 175 " --> pdb=" O   TYR E 191 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   TYR E 191 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TRP E 177 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 177 through 182

    518 hydrogen bonds defined for protein.
    1464 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: 1.56

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3087
        1.34 -     1.46: 2299
        1.46 -     1.58: 4405
        1.58 -     1.70: 3
        1.70 -     1.83: 90
  Bond restraints: 9884
  Sorted by residual:
  bond pdb=" O5' GDP A 401 "
       pdb=" PA  GDP A 401 "
    ideal  model  delta    sigma   weight residual
    1.610  1.826 -0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" O3A GDP A 401 "
       pdb=" PB  GDP A 401 "
    ideal  model  delta    sigma   weight residual
    1.610  1.726 -0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" C1  YN9 R 401 "
       pdb=" C3  YN9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.481  1.584 -0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" O5' GDP A 401 "
       pdb=" C5' GDP A 401 "
    ideal  model  delta    sigma   weight residual
    1.426  1.332  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C6  GDP A 401 "
       pdb=" N1  GDP A 401 "
    ideal  model  delta    sigma   weight residual
    1.337  1.425 -0.088 2.00e-02 2.50e+03 1.94e+01
  ... (remaining 9879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 13329
        3.17 -     6.34: 118
        6.34 -     9.52: 22
        9.52 -    12.69: 2
       12.69 -    15.86: 3
  Bond angle restraints: 13474
  Sorted by residual:
  angle pdb=" O5' GDP A 401 "
        pdb=" PA  GDP A 401 "
        pdb=" O2A GDP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50   93.64   15.86 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" O2B GDP A 401 "
        pdb=" PB  GDP A 401 "
        pdb=" O3A GDP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50   94.47   15.03 3.00e+00 1.11e-01 2.51e+01
  angle pdb=" O5' GDP A 401 "
        pdb=" PA  GDP A 401 "
        pdb=" O1A GDP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50   94.91   14.59 3.00e+00 1.11e-01 2.36e+01
  angle pdb=" C   LEU E 117 "
        pdb=" CA  LEU E 117 "
        pdb=" CB  LEU E 117 "
      ideal   model   delta    sigma   weight residual
     110.14  117.46   -7.32 1.54e+00 4.22e-01 2.26e+01
  angle pdb=" N   LEU E 117 "
        pdb=" CA  LEU E 117 "
        pdb=" C   LEU E 117 "
      ideal   model   delta    sigma   weight residual
     108.26  100.66    7.60 1.66e+00 3.63e-01 2.09e+01
  ... (remaining 13469 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.05: 5441
       20.05 -    40.10: 305
       40.10 -    60.14: 41
       60.14 -    80.19: 15
       80.19 -   100.24: 5
  Dihedral angle restraints: 5807
    sinusoidal: 2110
      harmonic: 3697
  Sorted by residual:
  dihedral pdb=" O2B GDP A 401 "
           pdb=" O3A GDP A 401 "
           pdb=" PB  GDP A 401 "
           pdb=" PA  GDP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   79.76  100.24     1      2.00e+01 2.50e-03 2.83e+01
  dihedral pdb=" C5' GDP A 401 "
           pdb=" O5' GDP A 401 "
           pdb=" PA  GDP A 401 "
           pdb=" O3A GDP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.98 -101.77  -78.25     1      2.00e+01 2.50e-03 1.91e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.13   19.87     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5804 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1358
       0.070 -    0.140: 201
       0.140 -    0.209: 12
       0.209 -    0.279: 4
       0.279 -    0.349: 2
  Chirality restraints: 1577
  Sorted by residual:
  chirality pdb=" CA  LEU R 245 "
            pdb=" N   LEU R 245 "
            pdb=" C   LEU R 245 "
            pdb=" CB  LEU R 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  TYR E 236 "
            pdb=" N   TYR E 236 "
            pdb=" C   TYR E 236 "
            pdb=" CB  TYR E 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  ASP B 291 "
            pdb=" N   ASP B 291 "
            pdb=" C   ASP B 291 "
            pdb=" CB  ASP B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1574 not shown)

  Planarity restraints: 1695
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 120 "   -0.052 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO A 121 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  74 "    0.015 2.00e-02 2.50e+03   1.61e-02 5.17e+00
        pdb=" CG  TYR A  74 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  74 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  74 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  74 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  74 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  74 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  74 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 163 "    0.035 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO A 164 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 164 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 164 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1692 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 123
        2.62 -     3.19: 8816
        3.19 -     3.76: 15550
        3.76 -     4.33: 21966
        4.33 -     4.90: 36550
  Nonbonded interactions: 83005
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 176 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" ND1 HIS R 112 "
            pdb=" O   CYS R 174 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OH  TYR A 153 "
            pdb=" OD1 ASP A 172 "
     model   vdw
     2.245 3.040
  ... (remaining 83000 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:             1.130
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
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   0.216   9886  Z= 0.302
  Angle     :  0.840  15.861  13478  Z= 0.443
  Chirality :  0.050   0.349   1577
  Planarity :  0.005   0.079   1695
  Dihedral  : 13.431 100.240   3411
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.24), residues: 1255
  helix:  1.09 (0.24), residues: 477
  sheet: -1.22 (0.28), residues: 298
  loop : -0.98 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.039   0.002   TYR A  74 
 PHE   0.018   0.002   PHE E  27 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 9884)
  covalent geometry    : angle       0.84014 (13474)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       0.61019 (    4)
  hydrogen bonds       : bond        0.13760 (  518)
  hydrogen bonds       : angle       6.17578 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.6635 (m-30) cc_final: 0.6429 (m-30)
REVERT: A  230 ASP cc_start: 0.5956 (t70) cc_final: 0.5423 (t70)
REVERT: A  278 MET cc_start: 0.5454 (mmp) cc_final: 0.5196 (ppp)
REVERT: R  221 LEU cc_start: 0.7530 (tp) cc_final: 0.7319 (tp)
REVERT: R  225 ILE cc_start: 0.7874 (mt) cc_final: 0.7673 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.6988
  time to fit residues: 118.6621
Evaluate side-chains
  125 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
R  80 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.153861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.124227 restraints weight = 14847.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.03
r_work: 0.3513 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9886  Z= 0.151
  Angle     :  0.628   9.480  13478  Z= 0.326
  Chirality :  0.044   0.180   1577
  Planarity :  0.005   0.053   1695
  Dihedral  :  7.171  96.115   1392
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.51 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.24), residues: 1255
  helix:  1.48 (0.24), residues: 482
  sheet: -0.92 (0.30), residues: 289
  loop : -1.08 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 143 
 TYR   0.035   0.002   TYR A  74 
 PHE   0.016   0.002   PHE E  29 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9884)
  covalent geometry    : angle       0.62814 (13474)
  SS BOND              : bond        0.00366 (    2)
  SS BOND              : angle       0.43251 (    4)
  hydrogen bonds       : bond        0.04099 (  518)
  hydrogen bonds       : angle       5.11365 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7936 (m-30) cc_final: 0.7698 (m-30)
REVERT: A   26 ASP cc_start: 0.7579 (m-30) cc_final: 0.7278 (m-30)
REVERT: A   53 MET cc_start: 0.7022 (mtp) cc_final: 0.6641 (mtp)
REVERT: A   74 TYR cc_start: 0.7231 (m-80) cc_final: 0.6974 (m-80)
REVERT: A   79 THR cc_start: 0.7982 (m) cc_final: 0.7775 (t)
REVERT: A  186 TYR cc_start: 0.7100 (t80) cc_final: 0.6781 (t80)
REVERT: A  208 ARG cc_start: 0.8537 (ptt-90) cc_final: 0.8293 (ptt-90)
REVERT: A  231 GLN cc_start: 0.5647 (pt0) cc_final: 0.5403 (pt0)
REVERT: A  278 MET cc_start: 0.6387 (mmp) cc_final: 0.5334 (ppp)
REVERT: R  225 ILE cc_start: 0.8312 (mt) cc_final: 0.8080 (mt)
REVERT: R  275 ILE cc_start: 0.8615 (mm) cc_final: 0.8318 (pt)
  outliers start: 19
  outliers final: 3
  residues processed: 153
  average time/residue: 0.6118
  time to fit residues: 99.9634
Evaluate side-chains
  130 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain R residue  179 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0060
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
E 113 GLN
R 322 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.152884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123293 restraints weight = 14783.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.01
r_work: 0.3511 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9886  Z= 0.160
  Angle     :  0.613   9.182  13478  Z= 0.316
  Chirality :  0.044   0.155   1577
  Planarity :  0.005   0.057   1695
  Dihedral  :  6.821  77.285   1392
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.81 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.24), residues: 1255
  helix:  1.66 (0.24), residues: 482
  sheet: -0.88 (0.30), residues: 288
  loop : -1.03 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 143 
 TYR   0.027   0.002   TYR R 247 
 PHE   0.017   0.002   PHE E  29 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9884)
  covalent geometry    : angle       0.61323 (13474)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.35764 (    4)
  hydrogen bonds       : bond        0.03912 (  518)
  hydrogen bonds       : angle       4.95020 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7942 (m-30) cc_final: 0.7727 (m-30)
REVERT: A   26 ASP cc_start: 0.7690 (m-30) cc_final: 0.7367 (m-30)
REVERT: A   53 MET cc_start: 0.6969 (mtp) cc_final: 0.6490 (mtp)
REVERT: A   74 TYR cc_start: 0.7220 (m-80) cc_final: 0.6945 (m-80)
REVERT: A   84 MET cc_start: 0.6525 (ttm) cc_final: 0.6274 (ttp)
REVERT: A  143 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6685 (ttp80)
REVERT: A  186 TYR cc_start: 0.7138 (t80) cc_final: 0.6697 (t80)
REVERT: A  208 ARG cc_start: 0.8523 (ptt-90) cc_final: 0.8262 (ptt-90)
REVERT: A  278 MET cc_start: 0.6456 (mmp) cc_final: 0.5368 (ppp)
REVERT: B   52 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8334 (mtp-110)
REVERT: R  221 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7572 (mp)
REVERT: R  225 ILE cc_start: 0.8347 (mt) cc_final: 0.8050 (mt)
REVERT: R  275 ILE cc_start: 0.8651 (mm) cc_final: 0.8335 (pt)
  outliers start: 26
  outliers final: 11
  residues processed: 149
  average time/residue: 0.6017
  time to fit residues: 95.9292
Evaluate side-chains
  140 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  221 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0030
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
E 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.154796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126232 restraints weight = 14899.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.08
r_work: 0.3515 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9886  Z= 0.147
  Angle     :  0.591   8.797  13478  Z= 0.306
  Chirality :  0.043   0.144   1577
  Planarity :  0.004   0.058   1695
  Dihedral  :  6.615  79.186   1392
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.31 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.24), residues: 1255
  helix:  1.75 (0.24), residues: 484
  sheet: -0.89 (0.29), residues: 288
  loop : -1.02 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.027   0.002   TYR R 247 
 PHE   0.015   0.002   PHE E  29 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9884)
  covalent geometry    : angle       0.59077 (13474)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       0.40467 (    4)
  hydrogen bonds       : bond        0.03704 (  518)
  hydrogen bonds       : angle       4.81755 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7689 (m-30) cc_final: 0.7378 (m-30)
REVERT: A   53 MET cc_start: 0.6996 (mtp) cc_final: 0.6657 (mtp)
REVERT: A   74 TYR cc_start: 0.7232 (m-80) cc_final: 0.6945 (m-80)
REVERT: A   84 MET cc_start: 0.6451 (ttm) cc_final: 0.6249 (ttp)
REVERT: A  143 ARG cc_start: 0.7062 (ttm110) cc_final: 0.6558 (ttp-170)
REVERT: A  186 TYR cc_start: 0.7095 (t80) cc_final: 0.6599 (t80)
REVERT: A  208 ARG cc_start: 0.8487 (ptt-90) cc_final: 0.8216 (ptt-90)
REVERT: A  231 GLN cc_start: 0.5684 (pt0) cc_final: 0.5424 (pt0)
REVERT: A  278 MET cc_start: 0.6377 (mmp) cc_final: 0.5472 (mpp)
REVERT: E  245 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7286 (tppp)
REVERT: R  221 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7612 (mp)
REVERT: R  225 ILE cc_start: 0.8336 (mt) cc_final: 0.8041 (mt)
REVERT: R  275 ILE cc_start: 0.8623 (mm) cc_final: 0.8275 (pt)
  outliers start: 32
  outliers final: 14
  residues processed: 152
  average time/residue: 0.5858
  time to fit residues: 95.2864
Evaluate side-chains
  143 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 44 optimal weight:    0.1980
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 155 ASN
E 113 GLN
R 232 GLN
R 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.154156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.125535 restraints weight = 15006.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.13
r_work: 0.3511 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9886  Z= 0.142
  Angle     :  0.580   8.528  13478  Z= 0.300
  Chirality :  0.043   0.140   1577
  Planarity :  0.004   0.060   1695
  Dihedral  :  6.413  80.826   1392
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.11 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.24), residues: 1255
  helix:  1.81 (0.24), residues: 485
  sheet: -0.89 (0.29), residues: 292
  loop : -0.95 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  32 
 TYR   0.026   0.002   TYR R 247 
 PHE   0.015   0.002   PHE E  29 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9884)
  covalent geometry    : angle       0.58010 (13474)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       0.41885 (    4)
  hydrogen bonds       : bond        0.03612 (  518)
  hydrogen bonds       : angle       4.75190 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7864 (m-30) cc_final: 0.7567 (m-30)
REVERT: A   26 ASP cc_start: 0.7709 (m-30) cc_final: 0.7411 (m-30)
REVERT: A   53 MET cc_start: 0.7044 (mtp) cc_final: 0.6517 (mtp)
REVERT: A   74 TYR cc_start: 0.7223 (m-80) cc_final: 0.6926 (m-80)
REVERT: A   84 MET cc_start: 0.6456 (ttm) cc_final: 0.6252 (ttp)
REVERT: A   88 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.5985 (tpp)
REVERT: A  186 TYR cc_start: 0.7029 (t80) cc_final: 0.6478 (t80)
REVERT: A  208 ARG cc_start: 0.8463 (ptt-90) cc_final: 0.8204 (ptt-90)
REVERT: A  278 MET cc_start: 0.6400 (mmp) cc_final: 0.5472 (mpp)
REVERT: B   52 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8369 (mtp-110)
REVERT: E   83 MET cc_start: 0.7001 (ttm) cc_final: 0.6789 (ttm)
REVERT: E  245 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7268 (tppp)
REVERT: R   36 ARG cc_start: 0.7774 (tpt170) cc_final: 0.7519 (tmt170)
REVERT: R  221 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7656 (mp)
REVERT: R  225 ILE cc_start: 0.8369 (mt) cc_final: 0.8071 (mt)
REVERT: R  275 ILE cc_start: 0.8632 (mm) cc_final: 0.8263 (pt)
  outliers start: 34
  outliers final: 14
  residues processed: 153
  average time/residue: 0.5747
  time to fit residues: 94.2745
Evaluate side-chains
  141 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 155 ASN
E 113 GLN
R 215 ASN
R 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.147439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.119874 restraints weight = 14836.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.93
r_work: 0.3475 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9886  Z= 0.209
  Angle     :  0.648   9.786  13478  Z= 0.331
  Chirality :  0.045   0.144   1577
  Planarity :  0.005   0.062   1695
  Dihedral  :  6.710  84.945   1392
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.22 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.24), residues: 1255
  helix:  1.69 (0.24), residues: 483
  sheet: -0.86 (0.29), residues: 288
  loop : -0.98 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 143 
 TYR   0.026   0.002   TYR R 247 
 PHE   0.021   0.002   PHE E  29 
 TRP   0.012   0.002   TRP B 211 
 HIS   0.006   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9884)
  covalent geometry    : angle       0.64799 (13474)
  SS BOND              : bond        0.00370 (    2)
  SS BOND              : angle       0.45278 (    4)
  hydrogen bonds       : bond        0.04055 (  518)
  hydrogen bonds       : angle       4.91124 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7943 (m-30) cc_final: 0.7631 (m-30)
REVERT: A   26 ASP cc_start: 0.7730 (m-30) cc_final: 0.7425 (m-30)
REVERT: A   29 LYS cc_start: 0.7945 (mptm) cc_final: 0.7596 (mmtm)
REVERT: A   53 MET cc_start: 0.7192 (mtp) cc_final: 0.6907 (mtp)
REVERT: A   74 TYR cc_start: 0.7151 (m-80) cc_final: 0.6848 (m-80)
REVERT: A   84 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6328 (ttp)
REVERT: A   88 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6000 (tpp)
REVERT: A  143 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6521 (ttp-170)
REVERT: A  208 ARG cc_start: 0.8462 (ptt-90) cc_final: 0.8156 (ptt-90)
REVERT: A  278 MET cc_start: 0.6428 (mmp) cc_final: 0.5484 (mpp)
REVERT: B   52 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8392 (mtp-110)
REVERT: E  245 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7204 (tppp)
REVERT: R  225 ILE cc_start: 0.8442 (mt) cc_final: 0.8112 (mt)
  outliers start: 32
  outliers final: 14
  residues processed: 145
  average time/residue: 0.5635
  time to fit residues: 87.6662
Evaluate side-chains
  136 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  232 GLN
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0770
   chunk 57 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 118 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.121623 restraints weight = 14819.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.05
r_work: 0.3512 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9886  Z= 0.150
  Angle     :  0.599   9.576  13478  Z= 0.307
  Chirality :  0.043   0.147   1577
  Planarity :  0.004   0.063   1695
  Dihedral  :  6.476  84.244   1392
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.72 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.24), residues: 1255
  helix:  1.78 (0.24), residues: 483
  sheet: -0.81 (0.30), residues: 287
  loop : -0.96 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.024   0.002   TYR R 247 
 PHE   0.014   0.001   PHE E  29 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9884)
  covalent geometry    : angle       0.59855 (13474)
  SS BOND              : bond        0.00360 (    2)
  SS BOND              : angle       0.52979 (    4)
  hydrogen bonds       : bond        0.03685 (  518)
  hydrogen bonds       : angle       4.76463 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7878 (m-30) cc_final: 0.7561 (m-30)
REVERT: A   26 ASP cc_start: 0.7696 (m-30) cc_final: 0.7387 (m-30)
REVERT: A   29 LYS cc_start: 0.7890 (mptm) cc_final: 0.7668 (mptm)
REVERT: A   53 MET cc_start: 0.7169 (mtp) cc_final: 0.6943 (mtm)
REVERT: A   74 TYR cc_start: 0.7165 (m-80) cc_final: 0.6847 (m-80)
REVERT: A   88 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5982 (tpp)
REVERT: A  143 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6428 (ttp-170)
REVERT: A  208 ARG cc_start: 0.8439 (ptt-90) cc_final: 0.8154 (ptt-90)
REVERT: B   52 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8359 (mtp-110)
REVERT: E  245 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7180 (tppp)
REVERT: R  221 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: R  225 ILE cc_start: 0.8374 (mt) cc_final: 0.8061 (mt)
  outliers start: 27
  outliers final: 14
  residues processed: 138
  average time/residue: 0.5899
  time to fit residues: 87.1910
Evaluate side-chains
  137 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  229 TYR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  232 GLN
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 155 ASN
R 322 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.149617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.121493 restraints weight = 14801.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.02
r_work: 0.3527 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9886  Z= 0.148
  Angle     :  0.597   9.229  13478  Z= 0.305
  Chirality :  0.043   0.143   1577
  Planarity :  0.004   0.065   1695
  Dihedral  :  6.404  83.198   1392
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.12 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.24), residues: 1255
  helix:  1.82 (0.24), residues: 483
  sheet: -0.79 (0.30), residues: 287
  loop : -0.93 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 143 
 TYR   0.025   0.002   TYR R 247 
 PHE   0.015   0.002   PHE E  29 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9884)
  covalent geometry    : angle       0.59704 (13474)
  SS BOND              : bond        0.00358 (    2)
  SS BOND              : angle       0.56028 (    4)
  hydrogen bonds       : bond        0.03655 (  518)
  hydrogen bonds       : angle       4.72238 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7863 (m-30) cc_final: 0.7558 (m-30)
REVERT: A   26 ASP cc_start: 0.7665 (m-30) cc_final: 0.7355 (m-30)
REVERT: A   29 LYS cc_start: 0.7834 (mptm) cc_final: 0.7601 (mptm)
REVERT: A   74 TYR cc_start: 0.7228 (m-80) cc_final: 0.6902 (m-80)
REVERT: A   88 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6013 (tpp)
REVERT: A  143 ARG cc_start: 0.6991 (ttm110) cc_final: 0.6495 (ttp-170)
REVERT: A  208 ARG cc_start: 0.8449 (ptt-90) cc_final: 0.8186 (ptt-90)
REVERT: A  278 MET cc_start: 0.6304 (mmp) cc_final: 0.5318 (mpp)
REVERT: B   52 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8360 (mtp-110)
REVERT: E  245 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7214 (tppp)
REVERT: R  225 ILE cc_start: 0.8368 (mt) cc_final: 0.8045 (mt)
  outliers start: 27
  outliers final: 18
  residues processed: 141
  average time/residue: 0.5624
  time to fit residues: 85.0240
Evaluate side-chains
  137 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  229 TYR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 120 optimal weight:    0.6980
   chunk 95 optimal weight:    0.0770
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 73 optimal weight:    0.1980
   chunk 54 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.150787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.122585 restraints weight = 14833.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.11
r_work: 0.3542 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9886  Z= 0.126
  Angle     :  0.580   8.917  13478  Z= 0.297
  Chirality :  0.042   0.150   1577
  Planarity :  0.004   0.066   1695
  Dihedral  :  6.212  80.157   1392
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.92 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.24), residues: 1255
  helix:  1.95 (0.24), residues: 483
  sheet: -0.68 (0.30), residues: 291
  loop : -0.87 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 143 
 TYR   0.024   0.001   TYR R 247 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9884)
  covalent geometry    : angle       0.57978 (13474)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       0.71669 (    4)
  hydrogen bonds       : bond        0.03504 (  518)
  hydrogen bonds       : angle       4.59845 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7817 (m-30) cc_final: 0.7509 (m-30)
REVERT: A   26 ASP cc_start: 0.7653 (m-30) cc_final: 0.7339 (m-30)
REVERT: A   29 LYS cc_start: 0.7820 (mptm) cc_final: 0.7446 (mmtm)
REVERT: A   74 TYR cc_start: 0.7156 (m-80) cc_final: 0.6863 (m-80)
REVERT: A   88 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5904 (tpp)
REVERT: A  143 ARG cc_start: 0.6852 (ttm110) cc_final: 0.6363 (ttp80)
REVERT: A  278 MET cc_start: 0.6264 (mmp) cc_final: 0.5298 (mpp)
REVERT: B   52 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8391 (mtp-110)
REVERT: E  245 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7228 (tppp)
REVERT: R  225 ILE cc_start: 0.8341 (mt) cc_final: 0.8034 (mt)
  outliers start: 23
  outliers final: 16
  residues processed: 135
  average time/residue: 0.5585
  time to fit residues: 80.9931
Evaluate side-chains
  139 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  229 TYR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 115 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 ASN
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.150330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122020 restraints weight = 14739.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.09
r_work: 0.3534 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9886  Z= 0.142
  Angle     :  0.599   8.928  13478  Z= 0.306
  Chirality :  0.043   0.176   1577
  Planarity :  0.004   0.067   1695
  Dihedral  :  6.234  78.803   1392
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.42 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.24), residues: 1255
  helix:  1.89 (0.24), residues: 483
  sheet: -0.71 (0.29), residues: 293
  loop : -0.86 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 143 
 TYR   0.024   0.002   TYR R 247 
 PHE   0.014   0.001   PHE E  29 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9884)
  covalent geometry    : angle       0.59848 (13474)
  SS BOND              : bond        0.00382 (    2)
  SS BOND              : angle       0.72338 (    4)
  hydrogen bonds       : bond        0.03587 (  518)
  hydrogen bonds       : angle       4.63146 ( 1464)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7807 (m-30) cc_final: 0.7498 (m-30)
REVERT: A   26 ASP cc_start: 0.7662 (m-30) cc_final: 0.7378 (m-30)
REVERT: A   74 TYR cc_start: 0.7138 (m-80) cc_final: 0.6845 (m-80)
REVERT: A   88 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5884 (tpp)
REVERT: A  143 ARG cc_start: 0.6836 (ttm110) cc_final: 0.6310 (ttp-170)
REVERT: A  278 MET cc_start: 0.6288 (mmp) cc_final: 0.5316 (mpp)
REVERT: B   52 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8363 (mtp-110)
REVERT: E  245 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7243 (tppp)
REVERT: R  225 ILE cc_start: 0.8325 (mt) cc_final: 0.8034 (mt)
  outliers start: 20
  outliers final: 16
  residues processed: 135
  average time/residue: 0.5569
  time to fit residues: 81.0450
Evaluate side-chains
  139 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  229 TYR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  245 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 78 optimal weight:    0.4980
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   chunk 81 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0370
   chunk 0 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 340 ASN
R 322 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.152031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.124154 restraints weight = 14858.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 2.05
r_work: 0.3563 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9886  Z= 0.117
  Angle     :  0.578   8.857  13478  Z= 0.295
  Chirality :  0.042   0.185   1577
  Planarity :  0.004   0.066   1695
  Dihedral  :  6.053  74.306   1392
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.42 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.24), residues: 1255
  helix:  1.99 (0.24), residues: 482
  sheet: -0.67 (0.29), residues: 293
  loop : -0.79 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 143 
 TYR   0.023   0.001   TYR R 247 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9884)
  covalent geometry    : angle       0.57761 (13474)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.79613 (    4)
  hydrogen bonds       : bond        0.03404 (  518)
  hydrogen bonds       : angle       4.54867 ( 1464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3774.24 seconds
wall clock time: 65 minutes 6.95 seconds (3906.95 seconds total)