Starting phenix.real_space_refine
on Sat Jun  7 15:03:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fu6_29453/06_2025/8fu6_29453_neut.cif"
  }
  resolution = 2.9
  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=   0.038
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      53      5.16       5
     C    5608      2.51       5
     N    1552      2.21       5
     O    1621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8834
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1773
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 205}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2597
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 240
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 2809
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2800
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 337}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 346, 2800
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 337}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 2870
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLN R  42 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN R  42 " occ=0.50
  Time building chain proxies: 6.73, per 1000 atoms: 0.76
  Number of scatterers: 8834
  At special positions: 0
  Unit cell: (84.348, 166.992, 101.388, 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      53     16.00
     O    1621      8.00
     N    1552      7.00
     C    5608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      41.4% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 4.178A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.752A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 239'
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.744A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.763A  pdb=" N   ASP A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.573A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.582A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.780A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.710A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.536A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.575A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.516A  pdb=" N   SER P  16 " --> pdb=" O   LYS P  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 43
      removed outlier: 3.571A  pdb=" N   PHE R  31 " --> pdb=" O   GLN R  27 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   CYS R  43 " --> pdb=" O   TYR R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 166
      removed outlier: 3.539A  pdb=" N   GLU R 133 " --> pdb=" O   GLU R 129 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA R 135 " --> pdb=" O   GLN R 131 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LYS R 136 " --> pdb=" O   LYS R 132 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   MET R 137 " --> pdb=" O   GLU R 133 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR R 138 " --> pdb=" O   VAL R 134 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU R 151 " --> pdb=" O   VAL R 147 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER R 152 " --> pdb=" O   GLY R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 197
    Processing helix  chain 'R' and resid 208 through 212
      removed outlier: 3.667A  pdb=" N   VAL R 212 " --> pdb=" O   ASP R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 221 through 255
      removed outlier: 3.687A  pdb=" N   ARG R 225 " --> pdb=" O   VAL R 221 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL R 226 " --> pdb=" O   ALA R 222 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA R 227 " --> pdb=" O   GLY R 223 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR R 239 " --> pdb=" O   ILE R 235 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   CYS R 240 " --> pdb=" O   VAL R 236 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   TRP R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU R 242 " --> pdb=" O   ASN R 238 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU R 243 " --> pdb=" O   TYR R 239 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU R 253 " --> pdb=" O   LEU R 249 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY R 254 " --> pdb=" O   HIS R 250 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU R 255 " --> pdb=" O   ASN R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 274
      removed outlier: 3.781A  pdb=" N   ALA R 274 " --> pdb=" O   ILE R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 289
      removed outlier: 3.789A  pdb=" N   VAL R 280 " --> pdb=" O   MET R 276 " (cutoff:3.500A)
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 292 through 296
      removed outlier: 4.225A  pdb=" N   THR R 296 " --> pdb=" O   GLN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 305
    Processing helix  chain 'R' and resid 308 through 335
      removed outlier: 3.588A  pdb=" N   ILE R 315 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE R 320 " --> pdb=" O   LEU R 316 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE R 321 " --> pdb=" O   ILE R 317 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 344 through 359
      removed outlier: 4.149A  pdb=" N   THR R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU R 352 " --> pdb=" O   ALA R 348 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR R 353 " --> pdb=" O   LYS R 349 " (cutoff:3.500A)
      Proline residue:  R 356  - end of helix
    Processing helix  chain 'R' and resid 360 through 365
      removed outlier: 4.097A  pdb=" N   PHE R 365 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 375 through 389
      removed outlier: 3.705A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS R 381 " --> pdb=" O   LEU R 377 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU R 386 " --> pdb=" O   LEU R 382 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 391 through 401
    Processing helix  chain 'R' and resid 404 through 421
      removed outlier: 3.564A  pdb=" N   GLU R 410 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG R 412 " --> pdb=" O   GLN R 408 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG R 413 " --> pdb=" O   SER R 409 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG R 414 " --> pdb=" O   GLU R 410 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TRP R 415 " --> pdb=" O   LEU R 411 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.611A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.806A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.945A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.317A  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 105
      removed outlier: 6.684A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.776A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.915A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.738A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.001A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.558A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.584A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA N  97 " --> pdb=" O   ASN N  35 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1095 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: 2.16

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2902
        1.35 -     1.47: 2266
        1.47 -     1.59: 3787
        1.59 -     1.71: 0
        1.71 -     1.83: 73
  Bond restraints: 9028
  Sorted by residual:
  bond pdb=" C   ALA R 274 "
       pdb=" N   PRO R 275 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.021 1.28e-02 6.10e+03 2.57e+00
  bond pdb=" CA  VAL A 224 "
       pdb=" CB  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.528  1.543 -0.015 1.34e-02 5.57e+03 1.30e+00
  bond pdb=" CA  VAL R 280 "
       pdb=" C   VAL R 280 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.009 8.80e-03 1.29e+04 1.13e+00
  bond pdb=" C   GLY N   9 "
       pdb=" O   GLY N   9 "
    ideal  model  delta    sigma   weight residual
    1.232  1.243 -0.011 1.03e-02 9.43e+03 1.11e+00
  bond pdb=" C   PHE B 235 "
       pdb=" N   PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.36e-02 5.41e+03 9.18e-01
  ... (remaining 9023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 11557
        1.20 -     2.40: 553
        2.40 -     3.60: 87
        3.60 -     4.80: 20
        4.80 -     6.00: 6
  Bond angle restraints: 12223
  Sorted by residual:
  angle pdb=" N   VAL N 110 "
        pdb=" CA  VAL N 110 "
        pdb=" C   VAL N 110 "
      ideal   model   delta    sigma   weight residual
     111.91  106.81    5.10 8.90e-01 1.26e+00 3.28e+01
  angle pdb=" N   VAL R 360 "
        pdb=" CA  VAL R 360 "
        pdb=" C   VAL R 360 "
      ideal   model   delta    sigma   weight residual
     113.39  108.93    4.46 1.47e+00 4.63e-01 9.20e+00
  angle pdb=" N   PHE A 315 "
        pdb=" CA  PHE A 315 "
        pdb=" C   PHE A 315 "
      ideal   model   delta    sigma   weight residual
     112.57  109.27    3.30 1.13e+00 7.83e-01 8.53e+00
  angle pdb=" N   TYR A  37 "
        pdb=" CA  TYR A  37 "
        pdb=" C   TYR A  37 "
      ideal   model   delta    sigma   weight residual
     111.28  114.37   -3.09 1.09e+00 8.42e-01 8.02e+00
  angle pdb=" CA  VAL R 360 "
        pdb=" C   VAL R 360 "
        pdb=" N   HIS R 361 "
      ideal   model   delta    sigma   weight residual
     118.55  116.14    2.41 8.60e-01 1.35e+00 7.87e+00
  ... (remaining 12218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 4899
       17.67 -    35.34: 368
       35.34 -    53.02: 47
       53.02 -    70.69: 7
       70.69 -    88.36: 6
  Dihedral angle restraints: 5327
    sinusoidal: 2102
      harmonic: 3225
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    1.91  -87.91     1      1.00e+01 1.00e-02 9.25e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.80  -38.80     1      1.00e+01 1.00e-02 2.12e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.07  -19.93     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5324 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 755
       0.025 -    0.050: 346
       0.050 -    0.076: 142
       0.076 -    0.101: 61
       0.101 -    0.126: 44
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CA  VAL N 110 "
            pdb=" N   VAL N 110 "
            pdb=" C   VAL N 110 "
            pdb=" CB  VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  TYR R 145 "
            pdb=" N   TYR R 145 "
            pdb=" C   TYR R 145 "
            pdb=" CB  TYR R 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R  81 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.87e+00
        pdb=" N   PRO R  82 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO R  82 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R  82 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 274 "   -0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO R 275 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 275 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 275 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 327 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO A 328 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 553
        2.74 -     3.28: 8226
        3.28 -     3.82: 13185
        3.82 -     4.36: 15566
        4.36 -     4.90: 28274
  Nonbonded interactions: 65804
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" NH1 ARG A  38 "
            pdb=" O   GLU R 260 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG1 THR B 221 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NH2 ARG R 201 "
            pdb=" OE1 GLN R 293 "
     model   vdw
     2.298 3.120
  ... (remaining 65799 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=0.50 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:             2.190
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.002   0.037   9031  Z= 0.133
  Angle     :  0.598   6.000  12229  Z= 0.367
  Chirality :  0.040   0.126   1348
  Planarity :  0.004   0.061   1562
  Dihedral  : 12.459  88.360   3232
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1091
  helix:  1.36 (0.26), residues: 425
  sheet:  0.43 (0.35), residues: 218
  loop : -1.48 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.014   0.001   TYR R 145 
 ARG   0.006   0.000   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22063 (  379)
  hydrogen bonds       : angle       5.97985 ( 1095)
  SS BOND              : bond        0.00516 (    3)
  SS BOND              : angle       0.88454 (    6)
  covalent geometry    : bond        0.00248 ( 9028)
  covalent geometry    : angle       0.59754 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.930 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 1.2298
  time to fit residues: 151.0861
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.5332

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B 237 ASN
R 131 GLN
R 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.176933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134803 restraints weight = 18822.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 3.39
r_work: 0.3268 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9031  Z= 0.112
  Angle     :  0.524   7.010  12229  Z= 0.284
  Chirality :  0.041   0.136   1348
  Planarity :  0.005   0.055   1562
  Dihedral  :  4.007  17.955   1213
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.09 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1091
  helix:  1.70 (0.26), residues: 429
  sheet:  0.51 (0.34), residues: 219
  loop : -1.46 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.028   0.001   TYR R 145 
 ARG   0.006   0.000   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05084 (  379)
  hydrogen bonds       : angle       4.22979 ( 1095)
  SS BOND              : bond        0.00537 (    3)
  SS BOND              : angle       0.84649 (    6)
  covalent geometry    : bond        0.00228 ( 9028)
  covalent geometry    : angle       0.52415 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.7046 (ttp-170) cc_final: 0.6445 (ttp80)
REVERT: B  152 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8206 (tt)
REVERT: N    3 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: P   17 ARG cc_start: 0.7249 (mmp-170) cc_final: 0.6452 (ttp-170)
REVERT: R  419 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.6331 (tpp-160)
  outliers start: 11
  outliers final: 4
  residues processed: 109
  average time/residue: 1.2443
  time to fit residues: 145.1874
Evaluate side-chains
  90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 85 optimal weight:    0.3980
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.172302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.128823 restraints weight = 28337.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 4.92
r_work: 0.3178 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9031  Z= 0.135
  Angle     :  0.561   9.690  12229  Z= 0.299
  Chirality :  0.042   0.138   1348
  Planarity :  0.004   0.052   1562
  Dihedral  :  4.221  20.355   1213
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.78 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1091
  helix:  1.80 (0.26), residues: 425
  sheet:  0.52 (0.34), residues: 222
  loop : -1.42 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.020   0.002   PHE N 108 
 TYR   0.029   0.002   TYR R 145 
 ARG   0.005   0.000   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05714 (  379)
  hydrogen bonds       : angle       3.97229 ( 1095)
  SS BOND              : bond        0.00794 (    3)
  SS BOND              : angle       1.12451 (    6)
  covalent geometry    : bond        0.00297 ( 9028)
  covalent geometry    : angle       0.56027 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.8728 (t0) cc_final: 0.8459 (t0)
REVERT: A  283 ARG cc_start: 0.7439 (ttm170) cc_final: 0.7133 (ttp-170)
REVERT: A  317 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.7069 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6927 (ttp-170) cc_final: 0.6466 (ttp80)
REVERT: B  152 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: R  334 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5582 (ttm170)
REVERT: R  419 ARG cc_start: 0.6676 (ttp-170) cc_final: 0.6239 (tpp-160)
  outliers start: 22
  outliers final: 8
  residues processed: 113
  average time/residue: 1.6632
  time to fit residues: 199.5399
Evaluate side-chains
  99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  296 THR
Chi-restraints excluded: chain R residue  334 ARG
Chi-restraints excluded: chain R residue  403 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
R 120 GLN
R 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.169809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.126860 restraints weight = 14249.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.68
r_work: 0.3204 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9031  Z= 0.149
  Angle     :  0.583   8.853  12229  Z= 0.313
  Chirality :  0.042   0.144   1348
  Planarity :  0.004   0.051   1562
  Dihedral  :  4.441  24.829   1213
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.22 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1091
  helix:  1.79 (0.26), residues: 424
  sheet:  0.53 (0.34), residues: 220
  loop : -1.43 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.028   0.002   TYR R 145 
 ARG   0.004   0.000   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06072 (  379)
  hydrogen bonds       : angle       3.96669 ( 1095)
  SS BOND              : bond        0.00644 (    3)
  SS BOND              : angle       1.82032 (    6)
  covalent geometry    : bond        0.00333 ( 9028)
  covalent geometry    : angle       0.58213 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7208 (mtm-85)
REVERT: B   19 ARG cc_start: 0.7085 (ttp-170) cc_final: 0.6606 (ttp80)
REVERT: B  152 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: B  234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8432 (t80)
REVERT: R  334 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5674 (ttm170)
REVERT: R  370 ASP cc_start: 0.7567 (t0) cc_final: 0.7344 (t0)
REVERT: R  419 ARG cc_start: 0.6740 (ttp-170) cc_final: 0.6292 (tpp-160)
  outliers start: 18
  outliers final: 8
  residues processed: 108
  average time/residue: 1.3458
  time to fit residues: 154.3437
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  296 THR
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 60 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0470
   chunk 22 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 86 optimal weight:    0.0670
   chunk 85 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 357 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.175085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.133357 restraints weight = 22169.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 4.22
r_work: 0.3253 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9031  Z= 0.094
  Angle     :  0.477   7.185  12229  Z= 0.256
  Chirality :  0.039   0.128   1348
  Planarity :  0.004   0.051   1562
  Dihedral  :  4.009  20.527   1213
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.59 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1091
  helix:  2.06 (0.26), residues: 432
  sheet:  0.61 (0.34), residues: 224
  loop : -1.46 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.023   0.001   TYR R 145 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  379)
  hydrogen bonds       : angle       3.60217 ( 1095)
  SS BOND              : bond        0.00351 (    3)
  SS BOND              : angle       0.95022 (    6)
  covalent geometry    : bond        0.00193 ( 9028)
  covalent geometry    : angle       0.47619 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7214 (mtm-85)
REVERT: A  356 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.7166 (pmt170)
REVERT: B   19 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6584 (ttp80)
REVERT: B  152 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8181 (tt)
REVERT: B  234 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8405 (t80)
REVERT: P   17 ARG cc_start: 0.7017 (mmp-170) cc_final: 0.6067 (ttp-170)
REVERT: R  419 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6264 (tpp-160)
  outliers start: 14
  outliers final: 8
  residues processed: 99
  average time/residue: 1.2227
  time to fit residues: 129.5152
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    0.0970
   chunk 88 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.167028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124742 restraints weight = 17253.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.18
r_work: 0.3122 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9031  Z= 0.150
  Angle     :  0.567   7.956  12229  Z= 0.303
  Chirality :  0.042   0.139   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  4.334  23.927   1213
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.12 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1091
  helix:  2.00 (0.25), residues: 424
  sheet:  0.62 (0.34), residues: 220
  loop : -1.43 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.023   0.002   PHE N 108 
 TYR   0.027   0.002   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05903 (  379)
  hydrogen bonds       : angle       3.80969 ( 1095)
  SS BOND              : bond        0.00734 (    3)
  SS BOND              : angle       1.62893 (    6)
  covalent geometry    : bond        0.00345 ( 9028)
  covalent geometry    : angle       0.56604 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7195 (mtm-85)
REVERT: B   19 ARG cc_start: 0.7030 (ttp-170) cc_final: 0.6547 (ttp80)
REVERT: B  152 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8117 (tt)
REVERT: B  225 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6360 (t70)
REVERT: B  234 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8455 (t80)
REVERT: R  334 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5703 (ttm170)
REVERT: R  370 ASP cc_start: 0.7576 (t0) cc_final: 0.7338 (t0)
REVERT: R  419 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6244 (tpp-160)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 1.3676
  time to fit residues: 153.9303
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  296 THR
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0010
   chunk 10 optimal weight:    0.0010
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.172661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.129590 restraints weight = 24520.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 4.18
r_work: 0.3202 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9031  Z= 0.094
  Angle     :  0.471   6.665  12229  Z= 0.254
  Chirality :  0.039   0.129   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  3.956  19.544   1213
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.97 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1091
  helix:  2.22 (0.26), residues: 432
  sheet:  0.73 (0.34), residues: 222
  loop : -1.44 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 289 
 TYR   0.024   0.001   TYR R 145 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03820 (  379)
  hydrogen bonds       : angle       3.50498 ( 1095)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       0.86369 (    6)
  covalent geometry    : bond        0.00197 ( 9028)
  covalent geometry    : angle       0.47047 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.7219 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6922 (ttp-170) cc_final: 0.6451 (ttp80)
REVERT: B   38 ASP cc_start: 0.7821 (p0) cc_final: 0.7427 (p0)
REVERT: B  152 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8084 (tt)
REVERT: B  225 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6077 (t70)
REVERT: B  234 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8341 (t80)
REVERT: P   17 ARG cc_start: 0.6872 (mmp-170) cc_final: 0.5830 (ttp-170)
REVERT: R  370 ASP cc_start: 0.7393 (t0) cc_final: 0.7168 (t0)
REVERT: R  419 ARG cc_start: 0.6850 (ttp-170) cc_final: 0.6169 (tpp-160)
  outliers start: 13
  outliers final: 6
  residues processed: 95
  average time/residue: 1.4150
  time to fit residues: 143.0283
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 77 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.168720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124592 restraints weight = 23619.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 4.05
r_work: 0.3147 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9031  Z= 0.127
  Angle     :  0.531   6.508  12229  Z= 0.284
  Chirality :  0.041   0.136   1348
  Planarity :  0.004   0.048   1562
  Dihedral  :  4.123  20.848   1213
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.29 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.25), residues: 1091
  helix:  2.16 (0.26), residues: 427
  sheet:  0.77 (0.34), residues: 214
  loop : -1.38 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.020   0.001   PHE N 108 
 TYR   0.027   0.001   TYR R 145 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05126 (  379)
  hydrogen bonds       : angle       3.63116 ( 1095)
  SS BOND              : bond        0.00654 (    3)
  SS BOND              : angle       1.46723 (    6)
  covalent geometry    : bond        0.00286 ( 9028)
  covalent geometry    : angle       0.53006 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7228 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6941 (ttp-170) cc_final: 0.6469 (ttp80)
REVERT: B  152 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8098 (tt)
REVERT: B  225 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7388 (m-70)
REVERT: B  234 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8386 (t80)
REVERT: P   17 ARG cc_start: 0.6993 (mmp-170) cc_final: 0.6007 (ttp-170)
REVERT: R  419 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6170 (tpp-160)
  outliers start: 15
  outliers final: 9
  residues processed: 100
  average time/residue: 1.2784
  time to fit residues: 136.6482
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  296 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0570
   chunk 10 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0870
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.171648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.128248 restraints weight = 23781.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 4.11
r_work: 0.3188 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9031  Z= 0.098
  Angle     :  0.477   5.840  12229  Z= 0.256
  Chirality :  0.039   0.129   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  3.932  18.883   1213
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.39 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1091
  helix:  2.26 (0.26), residues: 435
  sheet:  0.81 (0.34), residues: 220
  loop : -1.41 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.024   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  379)
  hydrogen bonds       : angle       3.45015 ( 1095)
  SS BOND              : bond        0.00464 (    3)
  SS BOND              : angle       0.98601 (    6)
  covalent geometry    : bond        0.00209 ( 9028)
  covalent geometry    : angle       0.47620 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.264 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6471 (ttp80)
REVERT: B  152 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8062 (tt)
REVERT: B  234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8377 (t80)
REVERT: P   17 ARG cc_start: 0.6912 (mmp-170) cc_final: 0.6420 (mmt90)
REVERT: R  419 ARG cc_start: 0.6896 (ttp-170) cc_final: 0.6194 (tpp-160)
  outliers start: 15
  outliers final: 8
  residues processed: 91
  average time/residue: 1.3542
  time to fit residues: 131.5181
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   chunk 86 optimal weight:    0.0030
   chunk 106 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.1794

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.167673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.123642 restraints weight = 21348.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.80
r_work: 0.3114 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9031  Z= 0.139
  Angle     :  0.551   6.374  12229  Z= 0.295
  Chirality :  0.041   0.138   1348
  Planarity :  0.004   0.048   1562
  Dihedral  :  4.201  21.417   1213
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.81 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1091
  helix:  2.17 (0.25), residues: 428
  sheet:  0.71 (0.34), residues: 220
  loop : -1.36 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  63 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.027   0.002   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05533 (  379)
  hydrogen bonds       : angle       3.68649 ( 1095)
  SS BOND              : bond        0.00709 (    3)
  SS BOND              : angle       1.62961 (    6)
  covalent geometry    : bond        0.00318 ( 9028)
  covalent geometry    : angle       0.55008 (12223)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.6978 (ttp-170) cc_final: 0.6509 (ttp80)
REVERT: B  152 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8117 (tt)
REVERT: B  234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8401 (t80)
REVERT: P   17 ARG cc_start: 0.7034 (mmp-170) cc_final: 0.6066 (ttp-170)
REVERT: R  296 THR cc_start: 0.8191 (m) cc_final: 0.7749 (m)
REVERT: R  410 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: R  419 ARG cc_start: 0.6935 (ttp-170) cc_final: 0.6245 (tpp-160)
  outliers start: 11
  outliers final: 8
  residues processed: 99
  average time/residue: 1.3498
  time to fit residues: 142.2436
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 85 optimal weight:    0.1980
   chunk 63 optimal weight:    0.0670
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.168761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.120566 restraints weight = 20298.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 3.46
r_work: 0.3125 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9031  Z= 0.114
  Angle     :  0.509   6.046  12229  Z= 0.273
  Chirality :  0.040   0.133   1348
  Planarity :  0.004   0.048   1562
  Dihedral  :  4.102  20.341   1213
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 15.13 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.25), residues: 1091
  helix:  2.28 (0.26), residues: 428
  sheet:  0.83 (0.35), residues: 214
  loop : -1.39 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.025   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  379)
  hydrogen bonds       : angle       3.59392 ( 1095)
  SS BOND              : bond        0.00582 (    3)
  SS BOND              : angle       1.27945 (    6)
  covalent geometry    : bond        0.00250 ( 9028)
  covalent geometry    : angle       0.50796 (12223)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7094.65 seconds
wall clock time: 122 minutes 11.95 seconds (7331.95 seconds total)