Starting phenix.real_space_refine
on Tue Mar  3 17:16:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2026/7x1u_32950.map"
  }
  resolution = 3.19
  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=   0.001 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    4782      2.51       5
     N    1276      2.21       5
     O    1384      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7483
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 302
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
    Chain: "A"
      Number of atoms: 1918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1918
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 275
          Unresolved non-hydrogen angles: 352
          Unresolved non-hydrogen dihedrals: 246
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'TYR:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 3, 'TRP:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 5}
          Unresolved non-hydrogen planarities: 150
    Chain: "B"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1612
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 215}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 137
    Chain: "C"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2269
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Unresolved non-hydrogen bonds: 267
          Unresolved non-hydrogen angles: 326
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 9, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 193
    Chain: "D"
      Number of atoms: 1356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1356
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 10, 'TRANS': 197}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 253
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 212
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 157
    Chain: "E"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 25
          Classifications: {'peptide': 3}
          Link IDs: {'PCIS': 1, 'TRANS': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.57, per 1000 atoms: 0.21
  Number of scatterers: 7483
  At special positions: 0
  Unit cell: (85.6, 113.42, 125.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1384      8.00
     N    1276      7.00
     C    4782      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 179 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 250.1 milliseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  PRO E   3 "
  Number of C-beta restraints generated:  2022

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 16 sheets defined
      29.0% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'F' and resid 12 through 17
      removed outlier: 3.574A  pdb=" N   GLU F  17 " --> pdb=" O   ARG F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 37
    Processing helix  chain 'F' and resid 38 through 41
    Processing helix  chain 'A' and resid 28 through 51
      removed outlier: 3.752A  pdb=" N   VAL A  32 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLY A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A  39 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A  40 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A  49 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 3.525A  pdb=" N   TYR A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A  64 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 59 through 64'
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 4.083A  pdb=" N   VAL A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 3.570A  pdb=" N   SER A  86 " --> pdb=" O   ASN A  82 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 3.628A  pdb=" N   ASN A 110 " --> pdb=" O   TYR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.695A  pdb=" N   ILE A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
      removed outlier: 3.865A  pdb=" N   PHE A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 136 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 131 through 136'
    Processing helix  chain 'A' and resid 138 through 155
      removed outlier: 4.160A  pdb=" N   LYS A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 4.212A  pdb=" N   PHE A 162 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 197
      removed outlier: 3.743A  pdb=" N   MET A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASP A 195 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 219
      removed outlier: 3.596A  pdb=" N   MET A 204 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A 213 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ILE A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.916A  pdb=" N   VAL A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   TRP A 279 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 289
      removed outlier: 3.893A  pdb=" N   ARG A 283 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
      removed outlier: 4.679A  pdb=" N   ILE A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
      removed outlier: 3.579A  pdb=" N   ASN A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      Proline residue:  A 317  - end of helix
      removed outlier: 3.539A  pdb=" N   TYR A 320 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
      removed outlier: 3.507A  pdb=" N   ARG A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 20
      removed outlier: 3.753A  pdb=" N   ASP B  20 " --> pdb=" O   SER B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.901A  pdb=" N   ILE B  49 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.943A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 130
    Processing helix  chain 'B' and resid 145 through 148
    Processing helix  chain 'B' and resid 149 through 154
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.691A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
      removed outlier: 4.250A  pdb=" N   ALA B 168 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 165 through 168'
    Processing helix  chain 'B' and resid 183 through 202
      removed outlier: 3.770A  pdb=" N   ALA B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 236
      removed outlier: 4.259A  pdb=" N   ASP B 230 " --> pdb=" O   ARG B 226 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ASP B 233 " --> pdb=" O   ASN B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 243
      removed outlier: 3.549A  pdb=" N   TYR B 243 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 26
      removed outlier: 3.857A  pdb=" N   ILE C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP C  20 " --> pdb=" O   ASN C  16 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA C  24 " --> pdb=" O   ASP C  20 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   CYS C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.728A  pdb=" N   SER D  31 " --> pdb=" O   ALA D  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171
      removed outlier: 3.971A  pdb=" N   ASN A 167 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 178 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA A 174 " --> pdb=" O   TYR A 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 76
      removed outlier: 3.957A  pdb=" N   LEU B  38 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 143 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62
      removed outlier: 3.992A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 105
      removed outlier: 3.581A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121
    Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 157
      removed outlier: 3.666A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.903A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER C 201 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.791A  pdb=" N   PHE C 241 " --> pdb=" O   PHE C 253 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.354A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 319 through 320
    Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 34
      removed outlier: 3.950A  pdb=" N   SER D  99 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49
      removed outlier: 6.575A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 148
    Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163
    Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 166

    204 hydrogen bonds defined for protein.
    549 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: 0.93

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1227
        1.31 -     1.43: 2053
        1.43 -     1.56: 4283
        1.56 -     1.69: 7
        1.69 -     1.82: 53
  Bond restraints: 7623
  Sorted by residual:
  bond pdb=" C   PCA E   1 "
       pdb=" N   HIS E   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.499 -0.170 1.40e-02 5.10e+03 1.47e+02
  bond pdb=" C   HIS E   2 "
       pdb=" N   PRO E   3 "
    ideal  model  delta    sigma   weight residual
    1.341  1.507 -0.166 1.60e-02 3.91e+03 1.08e+02
  bond pdb=" CA  PRO E   3 "
       pdb=" CB  PRO E   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.352  0.178 2.00e-02 2.50e+03 7.95e+01
  bond pdb=" CA  PCA E   1 "
       pdb=" CB  PCA E   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.369  0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" N   PCA E   1 "
       pdb=" CA  PCA E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.590 -0.132 1.90e-02 2.77e+03 4.82e+01
  ... (remaining 7618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 10182
        2.74 -     5.48: 218
        5.48 -     8.21: 33
        8.21 -    10.95: 10
       10.95 -    13.69: 2
  Bond angle restraints: 10445
  Sorted by residual:
  angle pdb=" N   VAL A  49 "
        pdb=" CA  VAL A  49 "
        pdb=" C   VAL A  49 "
      ideal   model   delta    sigma   weight residual
     111.90  107.34    4.56 8.10e-01 1.52e+00 3.16e+01
  angle pdb=" N   TYR A 181 "
        pdb=" CA  TYR A 181 "
        pdb=" C   TYR A 181 "
      ideal   model   delta    sigma   weight residual
     108.23  115.97   -7.74 1.38e+00 5.25e-01 3.14e+01
  angle pdb=" N   VAL A 264 "
        pdb=" CA  VAL A 264 "
        pdb=" C   VAL A 264 "
      ideal   model   delta    sigma   weight residual
     112.83  107.32    5.51 9.90e-01 1.02e+00 3.10e+01
  angle pdb=" N   ILE B 227 "
        pdb=" CA  ILE B 227 "
        pdb=" C   ILE B 227 "
      ideal   model   delta    sigma   weight residual
     112.96  107.47    5.49 1.00e+00 1.00e+00 3.02e+01
  angle pdb=" C   ASP C 195 "
        pdb=" N   THR C 196 "
        pdb=" CA  THR C 196 "
      ideal   model   delta    sigma   weight residual
     121.54  132.01  -10.47 1.91e+00 2.74e-01 3.00e+01
  ... (remaining 10440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 3945
       16.39 -    32.78: 386
       32.78 -    49.17: 68
       49.17 -    65.56: 4
       65.56 -    81.95: 2
  Dihedral angle restraints: 4405
    sinusoidal: 1282
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" C   HIS E   2 "
           pdb=" N   HIS E   2 "
           pdb=" CA  HIS E   2 "
           pdb=" CB  HIS E   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.12   14.52     0      2.50e+00 1.60e-01 3.37e+01
  dihedral pdb=" CA  TYR D 223 "
           pdb=" C   TYR D 223 "
           pdb=" N   PRO D 224 "
           pdb=" CA  PRO D 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.86  -26.14     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE D 108 "
           pdb=" C   PHE D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 4402 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.076: 1283
       1.076 -    2.151: 0
       2.151 -    3.226: 0
       3.226 -    4.302: 0
       4.302 -    5.377: 1
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  PRO E   3 "
            pdb=" N   PRO E   3 "
            pdb=" C   PRO E   3 "
            pdb=" CB  PRO E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.66    5.38 2.00e-01 2.50e+01 7.23e+02
  chirality pdb=" CA  HIS E   2 "
            pdb=" N   HIS E   2 "
            pdb=" C   HIS E   2 "
            pdb=" CB  HIS E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  PCA E   1 "
            pdb=" N   PCA E   1 "
            pdb=" C   PCA E   1 "
            pdb=" CB  PCA E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1331
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 316 "    0.058 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO A 317 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 187 "   -0.057 5.00e-02 4.00e+02   8.70e-02 1.21e+01
        pdb=" N   PRO D 188 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO D 188 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 188 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 223 "   -0.052 5.00e-02 4.00e+02   7.70e-02 9.48e+00
        pdb=" N   PRO D 224 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO D 224 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO D 224 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1328 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.16: 1
        2.16 -     2.85: 2708
        2.85 -     3.53: 9528
        3.53 -     4.22: 17568
        4.22 -     4.90: 29060
  Nonbonded interactions: 58865
  Sorted by model distance:
  nonbonded pdb=" C   PRO E   3 "
            pdb=" N   NH2 E   4 "
     model   vdw
     1.476 3.350
  nonbonded pdb=" NH2 ARG A 306 "
            pdb=" N   NH2 E   4 "
     model   vdw
     2.166 2.560
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NE  ARG A 306 "
            pdb=" N   NH2 E   4 "
     model   vdw
     2.273 2.560
  nonbonded pdb=" OG  SER C 227 "
            pdb=" OD1 ASP C 228 "
     model   vdw
     2.281 3.040
  ... (remaining 58860 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.178   7625  Z= 0.427
  Angle     :  1.029  13.689  10447  Z= 0.574
  Chirality :  0.161   5.377   1284
  Planarity :  0.007   0.087   1331
  Dihedral  : 13.418  81.955   2380
  Min Nonbonded Distance : 1.476

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.74 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 10.09 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -5.61 (0.19), residues: 1047
  helix: -4.86 (0.12), residues: 294
  sheet: -3.25 (0.31), residues: 214
  loop : -3.23 (0.22), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 283 
 TYR   0.023   0.002   TYR C  59 
 PHE   0.024   0.003   PHE D  27 
 TRP   0.020   0.003   TRP D  36 
 HIS   0.010   0.002   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00826 ( 7623)
  covalent geometry    : angle       1.02882 (10445)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       1.51844 (    2)
  hydrogen bonds       : bond        0.31558 (  204)
  hydrogen bonds       : angle      11.76200 (  549)
  Misc. bond           : bond        0.10662 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   49 ARG cc_start: 0.7806 (mpt90) cc_final: 0.7289 (mpp-170)
REVERT: D  110 PHE cc_start: 0.7172 (t80) cc_final: 0.6694 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 177
  average time/residue: 0.0910
  time to fit residues: 21.4121
Evaluate side-chains
  136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain C residue  315 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6902

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A 105 GLN
A 312 ASN
B  98 GLN
B 237 GLN
C  62 HIS
C  88 ASN
D 174 GLN
D 220 HIS
E   2 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.197478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.164032 restraints weight = 10674.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.4184 rms_B_bonded: 2.99
r_work: 0.4022 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7625  Z= 0.128
  Angle     :  0.683  17.461  10447  Z= 0.346
  Chirality :  0.045   0.206   1284
  Planarity :  0.006   0.069   1331
  Dihedral  :  6.314  28.556   1135
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.69 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.82 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -4.90 (0.21), residues: 1047
  helix: -3.96 (0.18), residues: 307
  sheet: -2.98 (0.29), residues: 241
  loop : -2.81 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 283 
 TYR   0.014   0.001   TYR D 102 
 PHE   0.021   0.001   PHE A 148 
 TRP   0.031   0.003   TRP D  47 
 HIS   0.006   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7623)
  covalent geometry    : angle       0.68308 (10445)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.40345 (    2)
  hydrogen bonds       : bond        0.04321 (  204)
  hydrogen bonds       : angle       7.01136 (  549)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8491 (mt) cc_final: 0.8286 (mm)
REVERT: A  216 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7678 (ttt180)
REVERT: A  310 TYR cc_start: 0.7761 (m-10) cc_final: 0.6847 (m-10)
REVERT: A  318 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8720 (m)
REVERT: B  232 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7731 (tttm)
REVERT: D  161 TYR cc_start: 0.6560 (m-80) cc_final: 0.6261 (m-80)
  outliers start: 20
  outliers final: 8
  residues processed: 160
  average time/residue: 0.0766
  time to fit residues: 17.0263
Evaluate side-chains
  142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 98 optimal weight:   30.0000
   chunk 91 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 3 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS
B  98 GLN
C 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.193189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.160462 restraints weight = 10625.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 3.04
r_work: 0.3966 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7625  Z= 0.179
  Angle     :  0.705  15.248  10447  Z= 0.352
  Chirality :  0.046   0.211   1284
  Planarity :  0.005   0.062   1331
  Dihedral  :  6.121  28.547   1134
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.64 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.81 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -4.44 (0.22), residues: 1047
  helix: -3.47 (0.20), residues: 311
  sheet: -2.75 (0.31), residues: 237
  loop : -2.58 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 306 
 TYR   0.020   0.002   TYR A 156 
 PHE   0.019   0.002   PHE A 148 
 TRP   0.030   0.003   TRP D  47 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7623)
  covalent geometry    : angle       0.70544 (10445)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.20625 (    2)
  hydrogen bonds       : bond        0.04041 (  204)
  hydrogen bonds       : angle       6.55350 (  549)
  Misc. bond           : bond        0.00067 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 TYR cc_start: 0.7785 (m-10) cc_final: 0.6868 (m-10)
REVERT: A  318 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8710 (m)
REVERT: B   21 LYS cc_start: 0.7011 (tptm) cc_final: 0.5707 (pttt)
REVERT: B   25 GLU cc_start: 0.7855 (pt0) cc_final: 0.7514 (pt0)
REVERT: B  232 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7812 (tttm)
REVERT: C  234 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6846 (t80)
REVERT: C  323 ASP cc_start: 0.7546 (p0) cc_final: 0.6730 (p0)
REVERT: D  110 PHE cc_start: 0.7173 (t80) cc_final: 0.6868 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 158
  average time/residue: 0.0746
  time to fit residues: 16.5631
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:   50.0000
   chunk 8 optimal weight:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.194496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.161943 restraints weight = 10843.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.98
r_work: 0.3990 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7625  Z= 0.145
  Angle     :  0.657  13.951  10447  Z= 0.330
  Chirality :  0.045   0.233   1284
  Planarity :  0.005   0.057   1331
  Dihedral  :  5.784  29.218   1134
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.56 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -4.07 (0.23), residues: 1047
  helix: -3.00 (0.23), residues: 311
  sheet: -2.69 (0.31), residues: 239
  loop : -2.37 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.019   0.001   TYR C 111 
 PHE   0.024   0.002   PHE B 228 
 TRP   0.032   0.003   TRP D  47 
 HIS   0.005   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7623)
  covalent geometry    : angle       0.65729 (10445)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.17713 (    2)
  hydrogen bonds       : bond        0.03436 (  204)
  hydrogen bonds       : angle       6.23819 (  549)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6421 (mm)
REVERT: A  310 TYR cc_start: 0.7706 (m-10) cc_final: 0.6869 (m-10)
REVERT: A  318 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (m)
REVERT: B   21 LYS cc_start: 0.6981 (tptm) cc_final: 0.5678 (pttt)
REVERT: B   25 GLU cc_start: 0.7890 (pt0) cc_final: 0.7551 (pt0)
REVERT: B  232 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7785 (tttm)
REVERT: C   49 ARG cc_start: 0.8156 (mpt90) cc_final: 0.7546 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6815 (t80)
REVERT: C  323 ASP cc_start: 0.7416 (p0) cc_final: 0.6648 (p0)
REVERT: D  110 PHE cc_start: 0.7389 (t80) cc_final: 0.7028 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0691
  time to fit residues: 15.5372
Evaluate side-chains
  154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   98 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 37 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0050
   chunk 24 optimal weight:    0.5980
   chunk 68 optimal weight:    7.9990
   chunk 1 optimal weight:   20.0000
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0030
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.2382

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.199871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.164844 restraints weight = 10749.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 3.31
r_work: 0.4047 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7625  Z= 0.098
  Angle     :  0.600  12.736  10447  Z= 0.300
  Chirality :  0.043   0.208   1284
  Planarity :  0.004   0.053   1331
  Dihedral  :  5.270  29.915   1134
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.20 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.63 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -3.57 (0.24), residues: 1047
  helix: -2.45 (0.25), residues: 312
  sheet: -2.37 (0.33), residues: 230
  loop : -2.21 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  72 
 TYR   0.023   0.001   TYR A 156 
 PHE   0.018   0.001   PHE B 228 
 TRP   0.035   0.002   TRP D  47 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7623)
  covalent geometry    : angle       0.60042 (10445)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.51784 (    2)
  hydrogen bonds       : bond        0.02909 (  204)
  hydrogen bonds       : angle       5.79696 (  549)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6442 (mm)
REVERT: A  310 TYR cc_start: 0.7782 (m-10) cc_final: 0.7037 (m-10)
REVERT: A  318 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8498 (m)
REVERT: B   21 LYS cc_start: 0.6816 (tptm) cc_final: 0.5758 (pttt)
REVERT: B  133 TRP cc_start: 0.8542 (m100) cc_final: 0.8301 (m100)
REVERT: B  142 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6788 (t80)
REVERT: C   49 ARG cc_start: 0.8060 (mpt90) cc_final: 0.7459 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7037 (t80)
REVERT: C  323 ASP cc_start: 0.7311 (p0) cc_final: 0.6604 (p0)
REVERT: D  110 PHE cc_start: 0.7034 (t80) cc_final: 0.6726 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 159
  average time/residue: 0.0739
  time to fit residues: 16.4213
Evaluate side-chains
  147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  98 GLN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.195012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.160782 restraints weight = 10765.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 3.09
r_work: 0.3981 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7625  Z= 0.149
  Angle     :  0.648  13.454  10447  Z= 0.323
  Chirality :  0.045   0.219   1284
  Planarity :  0.004   0.050   1331
  Dihedral  :  5.377  30.437   1134
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.49 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 24.16 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -3.47 (0.24), residues: 1047
  helix: -2.30 (0.26), residues: 312
  sheet: -2.36 (0.33), residues: 227
  loop : -2.18 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  52 
 TYR   0.023   0.001   TYR A 156 
 PHE   0.025   0.002   PHE A 148 
 TRP   0.036   0.002   TRP D  47 
 HIS   0.005   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7623)
  covalent geometry    : angle       0.64790 (10445)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.27923 (    2)
  hydrogen bonds       : bond        0.03225 (  204)
  hydrogen bonds       : angle       5.80280 (  549)
  Misc. bond           : bond        0.00023 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6460 (mm)
REVERT: A  310 TYR cc_start: 0.7725 (m-10) cc_final: 0.6911 (m-10)
REVERT: B   21 LYS cc_start: 0.6872 (tptm) cc_final: 0.5529 (pttt)
REVERT: B   25 GLU cc_start: 0.7899 (pt0) cc_final: 0.7540 (pt0)
REVERT: B  142 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7075 (t80)
REVERT: B  229 ASN cc_start: 0.7802 (p0) cc_final: 0.7509 (p0)
REVERT: C   49 ARG cc_start: 0.7888 (mpt90) cc_final: 0.7325 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6821 (t80)
REVERT: C  323 ASP cc_start: 0.7409 (p0) cc_final: 0.6689 (p0)
REVERT: D  110 PHE cc_start: 0.7223 (t80) cc_final: 0.6955 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0717
  time to fit residues: 15.8651
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 76 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.196513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.163533 restraints weight = 10736.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 2.86
r_work: 0.4027 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7625  Z= 0.127
  Angle     :  0.630  13.034  10447  Z= 0.314
  Chirality :  0.044   0.194   1284
  Planarity :  0.004   0.050   1331
  Dihedral  :  5.250  31.101   1134
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 24.16 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -3.23 (0.25), residues: 1047
  helix: -2.04 (0.26), residues: 314
  sheet: -2.14 (0.34), residues: 222
  loop : -2.12 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  52 
 TYR   0.026   0.001   TYR A 156 
 PHE   0.022   0.002   PHE A 148 
 TRP   0.041   0.003   TRP D  47 
 HIS   0.004   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7623)
  covalent geometry    : angle       0.63016 (10445)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.27617 (    2)
  hydrogen bonds       : bond        0.03010 (  204)
  hydrogen bonds       : angle       5.69021 (  549)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6447 (mm)
REVERT: A  310 TYR cc_start: 0.7691 (m-10) cc_final: 0.6960 (m-10)
REVERT: A  318 VAL cc_start: 0.8609 (p) cc_final: 0.8406 (m)
REVERT: B   21 LYS cc_start: 0.6791 (tptm) cc_final: 0.5458 (pttt)
REVERT: B   25 GLU cc_start: 0.7870 (pt0) cc_final: 0.7507 (pt0)
REVERT: B  142 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7041 (t80)
REVERT: B  229 ASN cc_start: 0.7762 (p0) cc_final: 0.7459 (p0)
REVERT: C   49 ARG cc_start: 0.7862 (mpt90) cc_final: 0.7295 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6915 (t80)
REVERT: C  323 ASP cc_start: 0.7402 (p0) cc_final: 0.6707 (p0)
REVERT: D  110 PHE cc_start: 0.7113 (t80) cc_final: 0.6732 (t80)
  outliers start: 30
  outliers final: 23
  residues processed: 156
  average time/residue: 0.0687
  time to fit residues: 15.3895
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0870
   chunk 80 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0170
   chunk 47 optimal weight:    0.9990
   chunk 87 optimal weight:    9.9990
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
C  75 GLN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.201432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.166502 restraints weight = 10820.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 2.98
r_work: 0.4074 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7625  Z= 0.096
  Angle     :  0.589  12.287  10447  Z= 0.293
  Chirality :  0.043   0.198   1284
  Planarity :  0.004   0.050   1331
  Dihedral  :  4.887  32.399   1134
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.16 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 25.23 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.87 (0.25), residues: 1047
  helix: -1.62 (0.28), residues: 308
  sheet: -1.98 (0.34), residues: 224
  loop : -1.98 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.027   0.001   TYR A 156 
 PHE   0.021   0.001   PHE A 148 
 TRP   0.043   0.002   TRP D  47 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7623)
  covalent geometry    : angle       0.58915 (10445)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.59112 (    2)
  hydrogen bonds       : bond        0.02707 (  204)
  hydrogen bonds       : angle       5.35960 (  549)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6581 (mm)
REVERT: A  310 TYR cc_start: 0.7705 (m-10) cc_final: 0.6911 (m-10)
REVERT: B   21 LYS cc_start: 0.6837 (tptm) cc_final: 0.5726 (pttt)
REVERT: B  133 TRP cc_start: 0.8548 (m100) cc_final: 0.8311 (m100)
REVERT: B  142 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.7005 (t80)
REVERT: B  229 ASN cc_start: 0.7693 (p0) cc_final: 0.7428 (p0)
REVERT: C   52 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7375 (mtt90)
REVERT: C  234 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.7030 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 163
  average time/residue: 0.0724
  time to fit residues: 16.7094
Evaluate side-chains
  154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 44 optimal weight:   30.0000
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0470
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.199032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.163998 restraints weight = 10800.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 3.11
r_work: 0.4040 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7625  Z= 0.109
  Angle     :  0.604  12.503  10447  Z= 0.300
  Chirality :  0.043   0.199   1284
  Planarity :  0.004   0.052   1331
  Dihedral  :  4.856  31.405   1134
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.68 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 24.92 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.75 (0.25), residues: 1047
  helix: -1.44 (0.28), residues: 314
  sheet: -1.85 (0.34), residues: 220
  loop : -1.99 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.027   0.001   TYR A 156 
 PHE   0.025   0.001   PHE A 148 
 TRP   0.044   0.002   TRP D  47 
 HIS   0.004   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7623)
  covalent geometry    : angle       0.60441 (10445)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.47819 (    2)
  hydrogen bonds       : bond        0.02757 (  204)
  hydrogen bonds       : angle       5.32420 (  549)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6567 (mm)
REVERT: A  310 TYR cc_start: 0.7713 (m-10) cc_final: 0.6916 (m-10)
REVERT: B   21 LYS cc_start: 0.6887 (tptm) cc_final: 0.5769 (pttt)
REVERT: B  142 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6839 (t80)
REVERT: B  229 ASN cc_start: 0.7676 (p0) cc_final: 0.7405 (p0)
REVERT: C   52 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7425 (mtt90)
REVERT: C  234 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6828 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 153
  average time/residue: 0.0732
  time to fit residues: 15.7595
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0470
   chunk 81 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    2.1884

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.192526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.158687 restraints weight = 10822.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 3.06
r_work: 0.3949 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7625  Z= 0.209
  Angle     :  0.704  13.536  10447  Z= 0.350
  Chirality :  0.047   0.220   1284
  Planarity :  0.005   0.054   1331
  Dihedral  :  5.392  30.761   1134
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.55 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 25.38 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.95 (0.25), residues: 1047
  helix: -1.68 (0.28), residues: 313
  sheet: -2.02 (0.34), residues: 215
  loop : -2.04 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  52 
 TYR   0.030   0.002   TYR A 156 
 PHE   0.025   0.002   PHE A 148 
 TRP   0.049   0.003   TRP D  47 
 HIS   0.006   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 7623)
  covalent geometry    : angle       0.70437 (10445)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.43620 (    2)
  hydrogen bonds       : bond        0.03397 (  204)
  hydrogen bonds       : angle       5.72918 (  549)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6599 (mm)
REVERT: A  310 TYR cc_start: 0.7644 (m-10) cc_final: 0.6769 (m-10)
REVERT: B   21 LYS cc_start: 0.7055 (tptm) cc_final: 0.6832 (tptm)
REVERT: B   25 GLU cc_start: 0.7974 (pt0) cc_final: 0.7595 (pt0)
REVERT: C   49 ARG cc_start: 0.7973 (mpt90) cc_final: 0.7468 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6763 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 148
  average time/residue: 0.0705
  time to fit residues: 14.7862
Evaluate side-chains
  153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   chunk 55 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0170
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4618

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.198888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.163453 restraints weight = 10773.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 3.25
r_work: 0.4036 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6789
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7625  Z= 0.105
  Angle     :  0.608  12.344  10447  Z= 0.302
  Chirality :  0.043   0.201   1284
  Planarity :  0.004   0.052   1331
  Dihedral  :  4.931  31.605   1134
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 25.84 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.62 (0.26), residues: 1047
  helix: -1.27 (0.29), residues: 311
  sheet: -1.87 (0.34), residues: 222
  loop : -1.91 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.027   0.001   TYR A 156 
 PHE   0.025   0.001   PHE A 148 
 TRP   0.049   0.002   TRP D  47 
 HIS   0.004   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7623)
  covalent geometry    : angle       0.60788 (10445)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.45011 (    2)
  hydrogen bonds       : bond        0.02761 (  204)
  hydrogen bonds       : angle       5.45705 (  549)
  Misc. bond           : bond        0.00002 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2230.48 seconds
wall clock time: 38 minutes 42.09 seconds (2322.09 seconds total)