Starting phenix.real_space_refine
on Sat Jul 26 18:43:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8guq_34276/07_2025/8guq_34276_neut.cif"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.042
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      66      5.16       5
     C    5602      2.51       5
     N    1499      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8789
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1721
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2250
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1760
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'KNF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.73, per 1000 atoms: 0.65
  Number of scatterers: 8789
  At special positions: 0
  Unit cell: (90.1334, 116.48, 131.733, 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      66     16.00
     O    1622      8.00
     N    1499      7.00
     C    5602      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 174 " - pdb=" SG  CYS R 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      37.8% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.708A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.824A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.585A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.194A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.506A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.943A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.959A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 3.533A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.850A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.544A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 3.542A  pdb=" N   ARG C  13 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 44
      removed outlier: 3.502A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 62
      removed outlier: 3.614A  pdb=" N   LEU R  39 " --> pdb=" O   ALA R  35 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR R  41 " --> pdb=" O   ALA R  37 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER R  47 " --> pdb=" O   LEU R  43 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU R  59 " --> pdb=" O   LEU R  55 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER R  61 " --> pdb=" O   LEU R  57 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   HIS R  62 " --> pdb=" O   ILE R  58 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 96
      removed outlier: 3.550A  pdb=" N   ILE R  73 " --> pdb=" O   SER R  69 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL R  92 " --> pdb=" O   ALA R  88 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASN R  93 " --> pdb=" O   CYS R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 117
      removed outlier: 3.712A  pdb=" N   VAL R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR R 114 " --> pdb=" O   ILE R 110 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR R 116 " --> pdb=" O   SER R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 137
      removed outlier: 3.502A  pdb=" N   CYS R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR R 137 " --> pdb=" O   LEU R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.602A  pdb=" N   VAL R 152 " --> pdb=" O   GLY R 148 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR R 153 " --> pdb=" O   ARG R 149 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU R 160 " --> pdb=" O   ILE R 156 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 224
      removed outlier: 3.702A  pdb=" N   LEU R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE R 200 " --> pdb=" O   LEU R 196 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   THR R 208 " --> pdb=" O   GLY R 204 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS R 217 " --> pdb=" O   LEU R 213 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   HIS R 219 " --> pdb=" O   LYS R 215 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 271
      removed outlier: 3.665A  pdb=" N   THR R 246 " --> pdb=" O   ARG R 242 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU R 249 " --> pdb=" O   LYS R 245 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU R 255 " --> pdb=" O   LEU R 251 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   CYS R 257 " --> pdb=" O   VAL R 253 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE R 259 " --> pdb=" O   LEU R 255 " (cutoff:3.500A)
      Proline residue:  R 260  - end of helix
      removed outlier: 4.246A  pdb=" N   LEU R 264 " --> pdb=" O   PRO R 260 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU R 269 " --> pdb=" O   MET R 265 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ALA R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR R 271 " --> pdb=" O   HIS R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 285
      removed outlier: 3.727A  pdb=" N   ALA R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE R 283 " --> pdb=" O   LYS R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 299
      removed outlier: 3.834A  pdb=" N   SER R 292 " --> pdb=" O   CYS R 288 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL R 294 " --> pdb=" O   ILE R 290 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN R 295 " --> pdb=" O   ASN R 291 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 303 through 317
      removed outlier: 3.518A  pdb=" N   HIS R 311 " --> pdb=" O   ARG R 307 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU R 314 " --> pdb=" O   ALA R 310 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA R 315 " --> pdb=" O   HIS R 311 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS R 316 " --> pdb=" O   HIS R 312 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.003A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.529A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.414A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.888A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.734A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.734A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 3.691A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.006A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.565A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.431A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.506A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.518A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.582A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR S 231 " --> pdb=" O   TYR S 215 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148

    357 hydrogen bonds defined for protein.
    1008 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.58

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2819
        1.35 -     1.47: 2323
        1.47 -     1.60: 3740
        1.60 -     1.73: 0
        1.73 -     1.86: 95
  Bond restraints: 8977
  Sorted by residual:
  bond pdb=" C11 KNF R 401 "
       pdb=" C5  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.482  1.342  0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" C10 KNF R 401 "
       pdb=" C6  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.359  0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" C10 KNF R 401 "
       pdb=" C9  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.533  1.437  0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" C5  KNF R 401 "
       pdb=" C6  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.331  0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" C4  KNF R 401 "
       pdb=" N2  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.399 -0.072 2.00e-02 2.50e+03 1.28e+01
  ... (remaining 8972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.00: 12115
        5.00 -    10.01: 47
       10.01 -    15.01: 4
       15.01 -    20.02: 1
       20.02 -    25.02: 1
  Bond angle restraints: 12168
  Sorted by residual:
  angle pdb=" C10 KNF R 401 "
        pdb=" C9  KNF R 401 "
        pdb=" C18 KNF R 401 "
      ideal   model   delta    sigma   weight residual
     118.74   93.72   25.02 3.00e+00 1.11e-01 6.96e+01
  angle pdb=" C18 KNF R 401 "
        pdb=" C8  KNF R 401 "
        pdb=" C7  KNF R 401 "
      ideal   model   delta    sigma   weight residual
     113.38  130.54  -17.16 3.00e+00 1.11e-01 3.27e+01
  angle pdb=" C   CYS A   3 "
        pdb=" N   THR A   4 "
        pdb=" CA  THR A   4 "
      ideal   model   delta    sigma   weight residual
     122.08  129.35   -7.27 1.47e+00 4.63e-01 2.45e+01
  angle pdb=" C   SER R  61 "
        pdb=" N   HIS R  62 "
        pdb=" CA  HIS R  62 "
      ideal   model   delta    sigma   weight residual
     122.08  129.33   -7.25 1.47e+00 4.63e-01 2.43e+01
  angle pdb=" CA  CYS R 174 "
        pdb=" CB  CYS R 174 "
        pdb=" SG  CYS R 174 "
      ideal   model   delta    sigma   weight residual
     114.40  124.73  -10.33 2.30e+00 1.89e-01 2.02e+01
  ... (remaining 12163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4706
       17.53 -    35.05: 502
       35.05 -    52.58: 97
       52.58 -    70.10: 18
       70.10 -    87.63: 5
  Dihedral angle restraints: 5328
    sinusoidal: 2044
      harmonic: 3284
  Sorted by residual:
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.22  -46.78     0      5.00e+00 4.00e-02 8.75e+01
  dihedral pdb=" CB  CYS R 174 "
           pdb=" SG  CYS R 174 "
           pdb=" SG  CYS R 179 "
           pdb=" CB  CYS R 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.31   71.69     1      1.00e+01 1.00e-02 6.58e+01
  dihedral pdb=" CA  HIS R  62 "
           pdb=" C   HIS R  62 "
           pdb=" N   GLN R  63 "
           pdb=" CA  GLN R  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 5325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.155: 1363
       0.155 -    0.310: 26
       0.310 -    0.465: 1
       0.465 -    0.619: 0
       0.619 -    0.774: 1
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" C8  KNF R 401 "
            pdb=" C18 KNF R 401 "
            pdb=" C7  KNF R 401 "
            pdb=" C9  KNF R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.65    1.88    0.77 2.00e-01 2.50e+01 1.50e+01
  chirality pdb=" C12 KNF R 401 "
            pdb=" C13 KNF R 401 "
            pdb=" C14 KNF R 401 "
            pdb=" N5  KNF R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.73    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER S 172 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO S 173 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO S 173 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO S 173 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 173 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.69e+00
        pdb=" C   THR R 173 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   THR R 173 "    0.017 2.00e-02 2.50e+03
        pdb=" N   CYS R 174 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 259 "   -0.042 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO R 260 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 260 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 260 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1522 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1966
        2.77 -     3.30: 7621
        3.30 -     3.84: 14430
        3.84 -     4.37: 17637
        4.37 -     4.90: 30843
  Nonbonded interactions: 72497
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.279 3.040
  ... (remaining 72492 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:             0.690
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.260
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
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      :  0.009   0.140   8980  Z= 0.381
  Angle     :  0.980  25.021  12174  Z= 0.504
  Chirality :  0.061   0.774   1391
  Planarity :  0.006   0.066   1525
  Dihedral  : 14.931  87.628   3201
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.47 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.16 (0.19), residues: 1117
  helix: -4.53 (0.11), residues: 379
  sheet: -2.72 (0.27), residues: 269
  loop : -2.63 (0.24), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B  63 
 HIS   0.009   0.002   HIS B 142 
 PHE   0.026   0.003   PHE S  27 
 TYR   0.037   0.003   TYR S 178 
 ARG   0.010   0.001   ARG R  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28849 (  357)
  hydrogen bonds       : angle      11.38282 ( 1008)
  SS BOND              : bond        0.00588 (    3)
  SS BOND              : angle       0.66365 (    6)
  covalent geometry    : bond        0.00893 ( 8977)
  covalent geometry    : angle       0.98034 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 183
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7478 (tp30)
REVERT: A  270 LYS cc_start: 0.7873 (mttt) cc_final: 0.7184 (mmtm)
REVERT: A  272 ASP cc_start: 0.7245 (m-30) cc_final: 0.6985 (p0)
REVERT: A  304 GLN cc_start: 0.7792 (tt0) cc_final: 0.7318 (tt0)
REVERT: A  331 ASN cc_start: 0.8276 (m-40) cc_final: 0.8042 (m110)
REVERT: A  346 ASN cc_start: 0.8438 (m-40) cc_final: 0.8047 (m-40)
REVERT: B   59 TYR cc_start: 0.8484 (m-80) cc_final: 0.7793 (m-80)
REVERT: B  232 ILE cc_start: 0.8415 (tt) cc_final: 0.7988 (tt)
REVERT: B  243 THR cc_start: 0.8717 (p) cc_final: 0.8363 (p)
REVERT: B  317 CYS cc_start: 0.7653 (p) cc_final: 0.7325 (p)
REVERT: B  335 PHE cc_start: 0.8278 (m-80) cc_final: 0.8077 (m-10)
REVERT: R   43 LEU cc_start: 0.8240 (mt) cc_final: 0.8018 (mt)
REVERT: R  302 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7492 (mmt90)
REVERT: S   18 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6933 (tpt170)
REVERT: S   46 GLU cc_start: 0.7783 (pt0) cc_final: 0.7510 (pt0)
REVERT: S   60 TYR cc_start: 0.8851 (m-80) cc_final: 0.8647 (m-80)
REVERT: S  190 ARG cc_start: 0.8206 (ptt-90) cc_final: 0.7996 (ptt90)
REVERT: S  198 THR cc_start: 0.7526 (t) cc_final: 0.6985 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 186
  average time/residue: 0.2653
  time to fit residues: 64.4681
Evaluate side-chains
  158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.0570
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0040
   overall best weight:    0.4110

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 213 HIS
A 255 ASN
B  62 HIS
B 183 HIS
B 340 ASN
C  24 ASN
R 218 GLN
R 295 ASN
R 316 HIS
S 130 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.188748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150193 restraints weight = 9337.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.89
r_work: 0.3494 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8980  Z= 0.131
  Angle     :  0.607  12.251  12174  Z= 0.316
  Chirality :  0.041   0.151   1391
  Planarity :  0.005   0.047   1525
  Dihedral  :  5.468  32.987   1246
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.49 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.21), residues: 1117
  helix: -2.72 (0.19), residues: 382
  sheet: -2.21 (0.28), residues: 268
  loop : -2.24 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.015   0.002   PHE A 189 
 TYR   0.022   0.001   TYR S 178 
 ARG   0.011   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04330 (  357)
  hydrogen bonds       : angle       5.66210 ( 1008)
  SS BOND              : bond        0.00505 (    3)
  SS BOND              : angle       0.73717 (    6)
  covalent geometry    : bond        0.00279 ( 8977)
  covalent geometry    : angle       0.60683 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 177
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8028 (tpp) cc_final: 0.7689 (tpp)
REVERT: A  270 LYS cc_start: 0.7917 (mttt) cc_final: 0.7087 (mmtm)
REVERT: A  304 GLN cc_start: 0.7833 (tt0) cc_final: 0.7439 (tt0)
REVERT: A  346 ASN cc_start: 0.8433 (m-40) cc_final: 0.8127 (m-40)
REVERT: B   59 TYR cc_start: 0.8580 (m-80) cc_final: 0.8154 (m-80)
REVERT: B   61 MET cc_start: 0.8659 (ppp) cc_final: 0.8420 (ppp)
REVERT: B  188 MET cc_start: 0.8240 (mmm) cc_final: 0.8033 (mmm)
REVERT: B  232 ILE cc_start: 0.8531 (tt) cc_final: 0.8167 (tt)
REVERT: C   13 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6762 (ttm110)
REVERT: R   22 MET cc_start: 0.8248 (tpp) cc_final: 0.7928 (tpp)
REVERT: R   43 LEU cc_start: 0.8313 (mt) cc_final: 0.8108 (mt)
REVERT: R   51 ASN cc_start: 0.7438 (m-40) cc_final: 0.7016 (m110)
REVERT: R  193 SER cc_start: 0.7794 (t) cc_final: 0.7541 (t)
REVERT: R  196 LEU cc_start: 0.7715 (mm) cc_final: 0.7442 (mm)
REVERT: S   46 GLU cc_start: 0.8463 (pt0) cc_final: 0.8117 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 184
  average time/residue: 0.2408
  time to fit residues: 59.1817
Evaluate side-chains
  164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0670
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  91 HIS
B 183 HIS
S 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.188108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149272 restraints weight = 9487.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.89
r_work: 0.3487 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8980  Z= 0.133
  Angle     :  0.572  11.371  12174  Z= 0.293
  Chirality :  0.041   0.154   1391
  Planarity :  0.004   0.046   1525
  Dihedral  :  5.108  29.453   1246
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.13 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.23), residues: 1117
  helix: -1.34 (0.23), residues: 385
  sheet: -2.02 (0.29), residues: 271
  loop : -2.00 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.025   0.001   TYR S 178 
 ARG   0.002   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03522 (  357)
  hydrogen bonds       : angle       4.98169 ( 1008)
  SS BOND              : bond        0.00407 (    3)
  SS BOND              : angle       0.82818 (    6)
  covalent geometry    : bond        0.00302 ( 8977)
  covalent geometry    : angle       0.57158 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  270 LYS cc_start: 0.7722 (mttt) cc_final: 0.6885 (mmtm)
REVERT: A  304 GLN cc_start: 0.7780 (tt0) cc_final: 0.7257 (tt0)
REVERT: B  188 MET cc_start: 0.8252 (mmm) cc_final: 0.8015 (mmm)
REVERT: B  234 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8522 (m-80)
REVERT: C   13 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6670 (ttm110)
REVERT: R   22 MET cc_start: 0.8469 (tpp) cc_final: 0.8133 (tpp)
REVERT: R   43 LEU cc_start: 0.8367 (mt) cc_final: 0.8115 (mt)
REVERT: R   51 ASN cc_start: 0.7251 (m-40) cc_final: 0.6906 (m110)
REVERT: R   70 TYR cc_start: 0.8667 (m-80) cc_final: 0.8183 (m-80)
REVERT: R  157 MET cc_start: 0.8063 (tmm) cc_final: 0.7593 (tmm)
REVERT: R  286 MET cc_start: 0.7452 (mmm) cc_final: 0.7034 (mmm)
REVERT: R  302 ARG cc_start: 0.7730 (ttm170) cc_final: 0.7192 (mtt90)
REVERT: S   46 GLU cc_start: 0.8408 (pt0) cc_final: 0.8167 (pt0)
REVERT: S  113 GLN cc_start: 0.8139 (mm110) cc_final: 0.7691 (mm-40)
REVERT: S  212 VAL cc_start: 0.8952 (t) cc_final: 0.8586 (m)
  outliers start: 22
  outliers final: 16
  residues processed: 170
  average time/residue: 0.2348
  time to fit residues: 53.6455
Evaluate side-chains
  165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0670
   chunk 91 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1924

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  13 GLN
B 183 HIS
S 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.184729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.148451 restraints weight = 9454.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.61
r_work: 0.3499 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8980  Z= 0.189
  Angle     :  0.608  13.297  12174  Z= 0.309
  Chirality :  0.043   0.162   1391
  Planarity :  0.004   0.045   1525
  Dihedral  :  5.119  28.445   1246
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.93 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.24), residues: 1117
  helix: -0.57 (0.25), residues: 385
  sheet: -1.95 (0.29), residues: 269
  loop : -1.84 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.022   0.002   PHE A 189 
 TYR   0.032   0.002   TYR A 230 
 ARG   0.003   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  357)
  hydrogen bonds       : angle       4.82376 ( 1008)
  SS BOND              : bond        0.00517 (    3)
  SS BOND              : angle       0.81871 (    6)
  covalent geometry    : bond        0.00444 ( 8977)
  covalent geometry    : angle       0.60745 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  270 LYS cc_start: 0.7816 (mttt) cc_final: 0.7036 (mmtm)
REVERT: A  304 GLN cc_start: 0.7845 (tt0) cc_final: 0.7274 (tt0)
REVERT: B   59 TYR cc_start: 0.8588 (m-80) cc_final: 0.8384 (m-80)
REVERT: B  188 MET cc_start: 0.8160 (mmm) cc_final: 0.7877 (mmm)
REVERT: B  232 ILE cc_start: 0.8573 (tt) cc_final: 0.8204 (tt)
REVERT: B  234 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (m-80)
REVERT: C   13 ARG cc_start: 0.7092 (ttm110) cc_final: 0.6736 (ttm110)
REVERT: R   43 LEU cc_start: 0.8442 (mt) cc_final: 0.8180 (mt)
REVERT: R   51 ASN cc_start: 0.7197 (m-40) cc_final: 0.6838 (m110)
REVERT: R   70 TYR cc_start: 0.8660 (m-80) cc_final: 0.8209 (m-80)
REVERT: R  157 MET cc_start: 0.8226 (tmm) cc_final: 0.7499 (tmm)
REVERT: R  170 MET cc_start: 0.6368 (mpp) cc_final: 0.5794 (pmm)
REVERT: S   21 SER cc_start: 0.7957 (t) cc_final: 0.7351 (p)
REVERT: S  212 VAL cc_start: 0.8908 (t) cc_final: 0.8553 (m)
  outliers start: 30
  outliers final: 24
  residues processed: 176
  average time/residue: 0.2351
  time to fit residues: 55.6877
Evaluate side-chains
  177 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 88 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 306 GLN
B 183 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.186438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.147932 restraints weight = 9358.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 1.76
r_work: 0.3493 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8980  Z= 0.145
  Angle     :  0.574  12.396  12174  Z= 0.290
  Chirality :  0.042   0.157   1391
  Planarity :  0.003   0.044   1525
  Dihedral  :  4.979  28.604   1246
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.67 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.24), residues: 1117
  helix: -0.10 (0.26), residues: 387
  sheet: -1.78 (0.30), residues: 267
  loop : -1.77 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.002   PHE S  27 
 TYR   0.026   0.002   TYR S 178 
 ARG   0.004   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03113 (  357)
  hydrogen bonds       : angle       4.62378 ( 1008)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       0.69928 (    6)
  covalent geometry    : bond        0.00336 ( 8977)
  covalent geometry    : angle       0.57360 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6660 (m) cc_final: 0.6228 (t)
REVERT: A  242 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7205 (mtm-85)
REVERT: A  270 LYS cc_start: 0.7707 (mttt) cc_final: 0.6916 (mmtm)
REVERT: A  304 GLN cc_start: 0.7829 (tt0) cc_final: 0.7213 (tt0)
REVERT: A  306 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7391 (mt0)
REVERT: B   59 TYR cc_start: 0.8592 (m-80) cc_final: 0.8302 (m-80)
REVERT: B  188 MET cc_start: 0.8211 (mmm) cc_final: 0.7929 (mmm)
REVERT: B  232 ILE cc_start: 0.8564 (tt) cc_final: 0.8207 (tt)
REVERT: B  234 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8516 (m-80)
REVERT: C   13 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6743 (ttm110)
REVERT: R   43 LEU cc_start: 0.8392 (mt) cc_final: 0.8102 (mt)
REVERT: R   70 TYR cc_start: 0.8645 (m-80) cc_final: 0.8327 (m-80)
REVERT: R  157 MET cc_start: 0.8111 (tmm) cc_final: 0.7215 (tmm)
REVERT: R  170 MET cc_start: 0.6736 (mpp) cc_final: 0.6295 (pmm)
REVERT: R  286 MET cc_start: 0.7581 (mmm) cc_final: 0.7167 (mmm)
REVERT: S   21 SER cc_start: 0.7899 (t) cc_final: 0.7304 (p)
REVERT: S  211 ASP cc_start: 0.8610 (m-30) cc_final: 0.8316 (m-30)
REVERT: S  212 VAL cc_start: 0.8780 (t) cc_final: 0.8523 (m)
  outliers start: 33
  outliers final: 26
  residues processed: 186
  average time/residue: 0.2614
  time to fit residues: 65.7930
Evaluate side-chains
  183 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.188797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148503 restraints weight = 9266.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.79
r_work: 0.3497 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8980  Z= 0.136
  Angle     :  0.577  12.488  12174  Z= 0.290
  Chirality :  0.042   0.197   1391
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.912  27.217   1246
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.62 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.25), residues: 1117
  helix:  0.17 (0.26), residues: 387
  sheet: -1.70 (0.30), residues: 267
  loop : -1.69 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE S  27 
 TYR   0.025   0.001   TYR S 178 
 ARG   0.004   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  357)
  hydrogen bonds       : angle       4.51717 ( 1008)
  SS BOND              : bond        0.01107 (    3)
  SS BOND              : angle       2.52090 (    6)
  covalent geometry    : bond        0.00313 ( 8977)
  covalent geometry    : angle       0.57415 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6619 (m) cc_final: 0.6193 (t)
REVERT: A  242 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7171 (mtm-85)
REVERT: A  270 LYS cc_start: 0.7727 (mttt) cc_final: 0.6938 (mmtm)
REVERT: A  304 GLN cc_start: 0.7749 (tt0) cc_final: 0.7181 (tt0)
REVERT: B   59 TYR cc_start: 0.8598 (m-80) cc_final: 0.8316 (m-80)
REVERT: B  188 MET cc_start: 0.8211 (mmm) cc_final: 0.7961 (mmm)
REVERT: B  232 ILE cc_start: 0.8558 (tt) cc_final: 0.8212 (tt)
REVERT: B  234 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8549 (m-80)
REVERT: C   13 ARG cc_start: 0.7096 (ttm110) cc_final: 0.6722 (ttm110)
REVERT: R   43 LEU cc_start: 0.8384 (mt) cc_final: 0.8101 (mt)
REVERT: R   70 TYR cc_start: 0.8484 (m-80) cc_final: 0.8177 (m-80)
REVERT: R  157 MET cc_start: 0.8188 (tmm) cc_final: 0.7230 (tmm)
REVERT: R  170 MET cc_start: 0.6727 (mpp) cc_final: 0.6353 (pmm)
REVERT: R  286 MET cc_start: 0.7693 (mmm) cc_final: 0.7442 (mmm)
REVERT: R  302 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7273 (mtt90)
REVERT: S   21 SER cc_start: 0.7894 (t) cc_final: 0.7297 (p)
REVERT: S  128 MET cc_start: 0.8323 (mmm) cc_final: 0.7332 (mmm)
REVERT: S  212 VAL cc_start: 0.8770 (t) cc_final: 0.8508 (m)
  outliers start: 31
  outliers final: 26
  residues processed: 176
  average time/residue: 0.3009
  time to fit residues: 71.3822
Evaluate side-chains
  179 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 71 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0970
   chunk 51 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 244 HIS
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.191455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152309 restraints weight = 9328.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.69
r_work: 0.3552 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8980  Z= 0.109
  Angle     :  0.549  12.342  12174  Z= 0.275
  Chirality :  0.041   0.188   1391
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.671  28.018   1245
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.68 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.25), residues: 1117
  helix:  0.41 (0.27), residues: 393
  sheet: -1.60 (0.29), residues: 270
  loop : -1.57 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.023   0.001   PHE A 189 
 TYR   0.022   0.001   TYR S 178 
 ARG   0.003   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02746 (  357)
  hydrogen bonds       : angle       4.33921 ( 1008)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       1.62318 (    6)
  covalent geometry    : bond        0.00248 ( 8977)
  covalent geometry    : angle       0.54834 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6676 (m) cc_final: 0.6175 (t)
REVERT: A  242 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7244 (mtm-85)
REVERT: A  270 LYS cc_start: 0.7869 (mttt) cc_final: 0.7162 (mmtm)
REVERT: A  304 GLN cc_start: 0.7848 (tt0) cc_final: 0.7214 (tt0)
REVERT: A  306 GLN cc_start: 0.7834 (mt0) cc_final: 0.7578 (mt0)
REVERT: B  188 MET cc_start: 0.8224 (mmm) cc_final: 0.7976 (mmm)
REVERT: B  232 ILE cc_start: 0.8524 (tt) cc_final: 0.8179 (tt)
REVERT: B  234 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8467 (m-80)
REVERT: C   13 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6747 (ttm110)
REVERT: R  157 MET cc_start: 0.8165 (tmm) cc_final: 0.7361 (tmm)
REVERT: R  170 MET cc_start: 0.6449 (mpp) cc_final: 0.6191 (pmm)
REVERT: R  293 MET cc_start: 0.7472 (ptp) cc_final: 0.6764 (mpp)
REVERT: S   87 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7187 (ptp-170)
REVERT: S  128 MET cc_start: 0.8251 (mmm) cc_final: 0.7285 (mmm)
REVERT: S  212 VAL cc_start: 0.8730 (t) cc_final: 0.8446 (m)
  outliers start: 22
  outliers final: 18
  residues processed: 179
  average time/residue: 0.2259
  time to fit residues: 54.6781
Evaluate side-chains
  170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0980
   chunk 102 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0170
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.191461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.152115 restraints weight = 9426.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 1.81
r_work: 0.3534 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8980  Z= 0.113
  Angle     :  0.559  12.286  12174  Z= 0.279
  Chirality :  0.042   0.195   1391
  Planarity :  0.003   0.042   1525
  Dihedral  :  4.617  31.539   1245
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.63 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 1117
  helix:  0.52 (0.27), residues: 400
  sheet: -1.47 (0.30), residues: 262
  loop : -1.56 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.013   0.001   PHE S  27 
 TYR   0.023   0.001   TYR A 230 
 ARG   0.005   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02741 (  357)
  hydrogen bonds       : angle       4.30789 ( 1008)
  SS BOND              : bond        0.00442 (    3)
  SS BOND              : angle       1.28044 (    6)
  covalent geometry    : bond        0.00256 ( 8977)
  covalent geometry    : angle       0.55844 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6608 (m) cc_final: 0.6085 (t)
REVERT: A  242 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7215 (mtm-85)
REVERT: A  270 LYS cc_start: 0.7782 (mttt) cc_final: 0.7050 (mmtm)
REVERT: A  304 GLN cc_start: 0.7744 (tt0) cc_final: 0.7094 (tt0)
REVERT: A  306 GLN cc_start: 0.7876 (mt0) cc_final: 0.7557 (mt0)
REVERT: B   20 ASP cc_start: 0.6694 (m-30) cc_final: 0.6383 (m-30)
REVERT: B  188 MET cc_start: 0.8251 (mmm) cc_final: 0.7987 (mmm)
REVERT: B  215 GLU cc_start: 0.8495 (tp30) cc_final: 0.8187 (tp30)
REVERT: B  232 ILE cc_start: 0.8568 (tt) cc_final: 0.8202 (tt)
REVERT: B  234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8516 (m-80)
REVERT: C   13 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6667 (ttm110)
REVERT: R  157 MET cc_start: 0.8130 (tmm) cc_final: 0.7363 (tmm)
REVERT: R  170 MET cc_start: 0.6448 (mpp) cc_final: 0.6222 (pmm)
REVERT: R  293 MET cc_start: 0.7576 (ptp) cc_final: 0.6680 (mpp)
REVERT: R  302 ARG cc_start: 0.7495 (ttm170) cc_final: 0.7182 (mtt90)
REVERT: S   87 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7162 (ptp-170)
REVERT: S  128 MET cc_start: 0.8287 (mmm) cc_final: 0.7282 (mmm)
REVERT: S  212 VAL cc_start: 0.8595 (t) cc_final: 0.8348 (m)
  outliers start: 25
  outliers final: 19
  residues processed: 173
  average time/residue: 0.2237
  time to fit residues: 52.3557
Evaluate side-chains
  173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0670
   chunk 62 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.189533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.151564 restraints weight = 9382.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.77
r_work: 0.3518 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8980  Z= 0.126
  Angle     :  0.570  13.031  12174  Z= 0.282
  Chirality :  0.042   0.197   1391
  Planarity :  0.003   0.041   1525
  Dihedral  :  4.601  31.886   1245
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.74 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.25), residues: 1117
  helix:  0.66 (0.27), residues: 400
  sheet: -1.44 (0.30), residues: 258
  loop : -1.49 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.027   0.001   PHE A 189 
 TYR   0.025   0.001   TYR S 178 
 ARG   0.004   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02758 (  357)
  hydrogen bonds       : angle       4.30395 ( 1008)
  SS BOND              : bond        0.00427 (    3)
  SS BOND              : angle       1.19178 (    6)
  covalent geometry    : bond        0.00291 ( 8977)
  covalent geometry    : angle       0.56997 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6697 (m) cc_final: 0.6186 (t)
REVERT: A  270 LYS cc_start: 0.7941 (mttt) cc_final: 0.7278 (mmtm)
REVERT: A  304 GLN cc_start: 0.7802 (tt0) cc_final: 0.7229 (tt0)
REVERT: A  306 GLN cc_start: 0.7825 (mt0) cc_final: 0.7579 (mt0)
REVERT: B   20 ASP cc_start: 0.6744 (m-30) cc_final: 0.6428 (m-30)
REVERT: B  188 MET cc_start: 0.8261 (mmm) cc_final: 0.7997 (mmm)
REVERT: B  215 GLU cc_start: 0.8445 (tp30) cc_final: 0.8206 (tp30)
REVERT: B  232 ILE cc_start: 0.8522 (tt) cc_final: 0.8175 (tt)
REVERT: B  234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8551 (m-80)
REVERT: C   13 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6760 (ttm110)
REVERT: R  157 MET cc_start: 0.8167 (tmm) cc_final: 0.7453 (tmm)
REVERT: R  293 MET cc_start: 0.7741 (ptp) cc_final: 0.6958 (mpp)
REVERT: R  302 ARG cc_start: 0.7514 (ttm170) cc_final: 0.7306 (mtt90)
REVERT: S   87 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7136 (ptp-170)
REVERT: S  128 MET cc_start: 0.8264 (mmm) cc_final: 0.7265 (mmm)
REVERT: S  212 VAL cc_start: 0.8734 (t) cc_final: 0.8472 (m)
REVERT: S  225 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (mt)
  outliers start: 26
  outliers final: 22
  residues processed: 171
  average time/residue: 0.2187
  time to fit residues: 50.8699
Evaluate side-chains
  173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 306 GLN
B 183 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.184824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146862 restraints weight = 9469.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.87
r_work: 0.3443 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8980  Z= 0.225
  Angle     :  0.639  14.245  12174  Z= 0.319
  Chirality :  0.045   0.201   1391
  Planarity :  0.004   0.047   1525
  Dihedral  :  4.885  30.925   1245
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.32 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.25), residues: 1117
  helix:  0.59 (0.27), residues: 400
  sheet: -1.65 (0.30), residues: 264
  loop : -1.55 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP S  47 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.018   0.002   PHE B 241 
 TYR   0.033   0.002   TYR S 178 
 ARG   0.004   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  357)
  hydrogen bonds       : angle       4.52994 ( 1008)
  SS BOND              : bond        0.00591 (    3)
  SS BOND              : angle       1.27073 (    6)
  covalent geometry    : bond        0.00531 ( 8977)
  covalent geometry    : angle       0.63841 (12168)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6713 (m) cc_final: 0.6256 (t)
REVERT: A  242 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.6814 (mtm-85)
REVERT: A  270 LYS cc_start: 0.7874 (mttt) cc_final: 0.7197 (mmtm)
REVERT: A  304 GLN cc_start: 0.7849 (tt0) cc_final: 0.7241 (tt0)
REVERT: B    9 GLN cc_start: 0.7893 (tt0) cc_final: 0.7386 (tm-30)
REVERT: B   20 ASP cc_start: 0.6722 (m-30) cc_final: 0.6398 (m-30)
REVERT: B  188 MET cc_start: 0.8323 (mmm) cc_final: 0.8014 (mmm)
REVERT: B  215 GLU cc_start: 0.8507 (tp30) cc_final: 0.8229 (tp30)
REVERT: B  234 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8600 (m-80)
REVERT: C   13 ARG cc_start: 0.7089 (ttm110) cc_final: 0.6735 (ttm110)
REVERT: R  157 MET cc_start: 0.8191 (tmm) cc_final: 0.7442 (tmm)
REVERT: R  293 MET cc_start: 0.7878 (ptp) cc_final: 0.7016 (mpp)
REVERT: R  302 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7350 (mtt90)
REVERT: S  128 MET cc_start: 0.8358 (mmm) cc_final: 0.7409 (mmm)
REVERT: S  157 ASN cc_start: 0.8288 (p0) cc_final: 0.7455 (p0)
REVERT: S  212 VAL cc_start: 0.8912 (t) cc_final: 0.8638 (m)
  outliers start: 27
  outliers final: 23
  residues processed: 175
  average time/residue: 0.2175
  time to fit residues: 52.1590
Evaluate side-chains
  174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 84 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 85 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.186294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146026 restraints weight = 9680.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.13
r_work: 0.3482 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8980  Z= 0.135
  Angle     :  0.593  13.049  12174  Z= 0.293
  Chirality :  0.042   0.182   1391
  Planarity :  0.003   0.038   1525
  Dihedral  :  4.722  31.484   1245
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.85 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.25), residues: 1117
  helix:  0.69 (0.27), residues: 400
  sheet: -1.57 (0.30), residues: 266
  loop : -1.50 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.027   0.001   PHE A 189 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.005   0.000   ARG R 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02851 (  357)
  hydrogen bonds       : angle       4.39598 ( 1008)
  SS BOND              : bond        0.00397 (    3)
  SS BOND              : angle       1.14767 (    6)
  covalent geometry    : bond        0.00313 ( 8977)
  covalent geometry    : angle       0.59285 (12168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6178.62 seconds
wall clock time: 111 minutes 4.47 seconds (6664.47 seconds total)