Starting phenix.real_space_refine
on Sun May 11 04:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j12_61065/05_2025/9j12_61065.cif"
  }
  resolution = 3.9
  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=   0.000 sd=   0.031
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      55      5.16       5
     C    4832      2.51       5
     N    1192      2.21       5
     O    1362      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7441
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 3721
          Classifications: {'peptide': 503}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 486}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3720
          Classifications: {'peptide': 504}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 487}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 4.78, per 1000 atoms: 0.64
  Number of scatterers: 7441
  At special positions: 0
  Unit cell: (90.2, 99, 106.7, 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      55     16.00
     O    1362      8.00
     N    1192      7.00
     C    4832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " 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: 1.95
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 3 sheets defined
      66.0% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 24
      removed outlier: 4.012A  pdb=" N   SER A  10 " --> pdb=" O   THR A   6 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TRP A  11 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER A  12 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   MET A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LYS A  15 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   HIS A  17 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A  21 " --> pdb=" O   HIS A  17 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 39 through 54
      removed outlier: 3.961A  pdb=" N   ARG A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 68
      removed outlier: 3.541A  pdb=" N   ASN A  61 " --> pdb=" O   ILE A  57 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'A' and resid 97 through 129
      removed outlier: 4.045A  pdb=" N   SER A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   MET A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A 124 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASN A 129 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.586A  pdb=" N   ALA A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 180
      removed outlier: 3.714A  pdb=" N   GLY A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA A 175 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 187
      removed outlier: 3.856A  pdb=" N   ARG A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
      removed outlier: 4.040A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
      removed outlier: 3.566A  pdb=" N   ALA A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   VAL A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS A 268 " --> pdb=" O   PHE A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.800A  pdb=" N   ILE A 278 " --> pdb=" O   MET A 274 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ILE A 284 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 309
      removed outlier: 4.013A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 330
      removed outlier: 4.048A  pdb=" N   ARG A 330 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 327 through 330'
    Processing helix  chain 'A' and resid 331 through 360
      removed outlier: 4.510A  pdb=" N   TRP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ALA A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU A 346 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU A 347 " --> pdb=" O   TYR A 343 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 358 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.999A  pdb=" N   TYR A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.539A  pdb=" N   LYS A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 3.510A  pdb=" N   MET A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 430
      removed outlier: 3.667A  pdb=" N   VAL A 430 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 427 through 430'
    Processing helix  chain 'A' and resid 438 through 449
      removed outlier: 3.822A  pdb=" N   LEU A 442 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 451
      No H-bonds generated for 'chain 'A' and resid 450 through 451'
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.531A  pdb=" N   ILE A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 478
      removed outlier: 4.358A  pdb=" N   THR A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ALA A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 480 through 495
      removed outlier: 3.950A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 505
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 4.322A  pdb=" N   SER B  12 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS B  17 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ASN B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 34 through 38
      removed outlier: 3.713A  pdb=" N   LYS B  37 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR B  38 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 34 through 38'
    Processing helix  chain 'B' and resid 40 through 55
      removed outlier: 4.027A  pdb=" N   LEU B  44 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ARG B  45 " --> pdb=" O   THR B  41 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 66
    Processing helix  chain 'B' and resid 73 through 77
      removed outlier: 3.972A  pdb=" N   CYS B  77 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.928A  pdb=" N   CYS B  90 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 86 through 91'
    Processing helix  chain 'B' and resid 95 through 128
      removed outlier: 3.566A  pdb=" N   ASP B 108 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL B 110 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET B 124 " --> pdb=" O   GLY B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
      removed outlier: 3.599A  pdb=" N   ILE B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 178
      removed outlier: 4.027A  pdb=" N   VAL B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU B 167 " --> pdb=" O   MET B 163 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA B 175 " --> pdb=" O   CYS B 171 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.636A  pdb=" N   ARG B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 208
      removed outlier: 3.985A  pdb=" N   ARG B 194 " --> pdb=" O   PRO B 190 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 249 through 267
      removed outlier: 3.632A  pdb=" N   TRP B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   MET B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 285
      removed outlier: 4.374A  pdb=" N   VAL B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
      removed outlier: 4.019A  pdb=" N   TYR B 307 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE B 308 " --> pdb=" O   ASN B 304 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR B 309 " --> pdb=" O   TYR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 358
      removed outlier: 3.748A  pdb=" N   VAL B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ALA B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR B 349 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TYR B 354 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   THR B 355 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
      removed outlier: 3.994A  pdb=" N   TYR B 375 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU B 376 " --> pdb=" O   TYR B 372 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.736A  pdb=" N   LEU B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 424
      removed outlier: 3.893A  pdb=" N   VAL B 414 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER B 423 " --> pdb=" O   TYR B 419 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
      Proline residue:  B 428  - end of helix
      No H-bonds generated for 'chain 'B' and resid 425 through 430'
    Processing helix  chain 'B' and resid 437 through 450
      removed outlier: 4.163A  pdb=" N   SER B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 474
      removed outlier: 3.654A  pdb=" N   ALA B 464 " --> pdb=" O   GLU B 460 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL B 465 " --> pdb=" O   THR B 461 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   THR B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 507
      removed outlier: 3.785A  pdb=" N   ILE B 484 " --> pdb=" O   ILE B 480 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   SER B 495 " --> pdb=" O   TYR B 491 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TYR B 497 " --> pdb=" O   ALA B 493 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASP B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   LEU B 501 " --> pdb=" O   TYR B 497 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY B 502 " --> pdb=" O   ASP B 498 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 235
      removed outlier: 6.457A  pdb=" N   GLU A 234 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 135
      removed outlier: 4.568A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 394 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 220

    335 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 2.26 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: 2300
        1.35 -     1.47: 1873
        1.47 -     1.59: 3326
        1.59 -     1.71: 1
        1.71 -     1.82: 93
  Bond restraints: 7593
  Sorted by residual:
  bond pdb=" CB  PRO A 296 "
       pdb=" CG  PRO A 296 "
    ideal  model  delta    sigma   weight residual
    1.492  1.649 -0.157 5.00e-02 4.00e+02 9.91e+00
  bond pdb=" N   PRO A 296 "
       pdb=" CA  PRO A 296 "
    ideal  model  delta    sigma   weight residual
    1.466  1.449  0.016 1.21e-02 6.83e+03 1.80e+00
  bond pdb=" CB  GLN B 191 "
       pdb=" CG  GLN B 191 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" C   VAL A 344 "
       pdb=" O   VAL A 344 "
    ideal  model  delta    sigma   weight residual
    1.231  1.244 -0.012 1.02e-02 9.61e+03 1.48e+00
  bond pdb=" CA  ASP A 455 "
       pdb=" CB  ASP A 455 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.26e+00
  ... (remaining 7588 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 10180
        2.85 -     5.71: 104
        5.71 -     8.56: 30
        8.56 -    11.42: 8
       11.42 -    14.27: 1
  Bond angle restraints: 10323
  Sorted by residual:
  angle pdb=" CA  PRO A 296 "
        pdb=" N   PRO A 296 "
        pdb=" CD  PRO A 296 "
      ideal   model   delta    sigma   weight residual
     112.00   97.73   14.27 1.40e+00 5.10e-01 1.04e+02
  angle pdb=" N   VAL B 176 "
        pdb=" CA  VAL B 176 "
        pdb=" C   VAL B 176 "
      ideal   model   delta    sigma   weight residual
     113.71  107.02    6.69 9.50e-01 1.11e+00 4.96e+01
  angle pdb=" C   LYS A  37 "
        pdb=" CA  LYS A  37 "
        pdb=" CB  LYS A  37 "
      ideal   model   delta    sigma   weight residual
     110.16  119.58   -9.42 1.44e+00 4.82e-01 4.28e+01
  angle pdb=" C   PRO A 296 "
        pdb=" CA  PRO A 296 "
        pdb=" CB  PRO A 296 "
      ideal   model   delta    sigma   weight residual
     111.12  103.30    7.82 1.29e+00 6.01e-01 3.68e+01
  angle pdb=" N   THR A  38 "
        pdb=" CA  THR A  38 "
        pdb=" CB  THR A  38 "
      ideal   model   delta    sigma   weight residual
     110.99  119.73   -8.74 1.77e+00 3.19e-01 2.44e+01
  ... (remaining 10318 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.11: 3996
       18.11 -    36.22: 338
       36.22 -    54.32: 83
       54.32 -    72.43: 4
       72.43 -    90.54: 4
  Dihedral angle restraints: 4425
    sinusoidal: 1590
      harmonic: 2835
  Sorted by residual:
  dihedral pdb=" CA  ARG A  36 "
           pdb=" C   ARG A  36 "
           pdb=" N   LYS A  37 "
           pdb=" CA  LYS A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.62  -27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CB  CYS B  77 "
           pdb=" SG  CYS B  77 "
           pdb=" SG  CYS B  90 "
           pdb=" CB  CYS B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.62  -39.62     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" CB  CYS A  77 "
           pdb=" SG  CYS A  77 "
           pdb=" SG  CYS A  90 "
           pdb=" CB  CYS A  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.47   39.53     1      1.00e+01 1.00e-02 2.20e+01
  ... (remaining 4422 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 790
       0.037 -    0.074: 354
       0.074 -    0.111: 84
       0.111 -    0.148: 17
       0.148 -    0.185: 5
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CB  VAL A 105 "
            pdb=" CA  VAL A 105 "
            pdb=" CG1 VAL A 105 "
            pdb=" CG2 VAL A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  HIS A 297 "
            pdb=" N   HIS A 297 "
            pdb=" C   HIS A 297 "
            pdb=" CB  HIS A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.87e-01
  chirality pdb=" CA  MET B  14 "
            pdb=" N   MET B  14 "
            pdb=" C   MET B  14 "
            pdb=" CB  MET B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  ... (remaining 1247 not shown)

  Planarity restraints: 1270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 295 "    0.124 5.00e-02 4.00e+02   1.76e-01 4.94e+01
        pdb=" N   PRO A 296 "   -0.303 5.00e-02 4.00e+02
        pdb=" CA  PRO A 296 "    0.094 5.00e-02 4.00e+02
        pdb=" CD  PRO A 296 "    0.085 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 130 "   -0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 131 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  17 "   -0.013 2.00e-02 2.50e+03   1.24e-02 2.32e+00
        pdb=" CG  HIS B  17 "    0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  17 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1267 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 157
        2.69 -     3.24: 7845
        3.24 -     3.80: 11186
        3.80 -     4.35: 14141
        4.35 -     4.90: 23041
  Nonbonded interactions: 56370
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  61 "
            pdb=" ND2 ASN B 141 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" OD2 ASP B 108 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OG1 THR B 192 "
            pdb=" OE1 GLU B 463 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU A 346 "
            pdb=" OG1 THR A 350 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASP A 345 "
            pdb=" OG1 THR A 349 "
     model   vdw
     2.277 3.040
  ... (remaining 56365 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 504 or (resid 505 through 507 and (name N or nam \ 
e CA or name C or name O or name CB ))))
  selection = (chain 'B' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 10 through 507))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.440
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.003   0.157   7599  Z= 0.154
  Angle     :  0.858  14.270  10335  Z= 0.489
  Chirality :  0.043   0.185   1250
  Planarity :  0.006   0.176   1270
  Dihedral  : 14.032  90.541   2609
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.70 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.11 %
  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: -2.39 (0.25), residues: 1003
  helix: -0.70 (0.21), residues: 555
  sheet:  None (None), residues: 0
  loop : -2.78 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 335 
 HIS   0.011   0.001   HIS B  17 
 PHE   0.026   0.001   PHE A 173 
 TYR   0.014   0.001   TYR A  56 
 ARG   0.006   0.001   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21812 (  335)
  hydrogen bonds       : angle       6.55178 (  996)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       1.55614 (   12)
  covalent geometry    : bond        0.00338 ( 7593)
  covalent geometry    : angle       0.85732 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 TRP cc_start: 0.7218 (m-90) cc_final: 0.6340 (m-90)
REVERT: A  356 MET cc_start: 0.7776 (mmm) cc_final: 0.7432 (mmp)
REVERT: A  375 TYR cc_start: 0.8192 (m-10) cc_final: 0.7977 (m-10)
REVERT: A  418 LEU cc_start: 0.8458 (mm) cc_final: 0.8103 (tt)
REVERT: A  444 MET cc_start: 0.8693 (tpp) cc_final: 0.8133 (tpp)
REVERT: B  168 LEU cc_start: 0.8323 (mt) cc_final: 0.7998 (mt)
REVERT: B  169 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: B  267 MET cc_start: 0.8497 (mmm) cc_final: 0.8083 (mmm)
REVERT: B  456 ILE cc_start: 0.8911 (mp) cc_final: 0.8617 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1722
  time to fit residues: 43.8139
Evaluate side-chains
  161 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.153415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.121241 restraints weight = 15402.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.124852 restraints weight = 8419.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.127133 restraints weight = 5648.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7599  Z= 0.125
  Angle     :  0.639   9.167  10335  Z= 0.316
  Chirality :  0.042   0.145   1250
  Planarity :  0.005   0.096   1270
  Dihedral  :  4.699  27.107   1061
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.22 %
    Favored  : 71.48 %
  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: -1.98 (0.26), residues: 1003
  helix: -0.31 (0.22), residues: 574
  sheet: -3.15 (1.55), residues: 10
  loop : -2.74 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B  17 
 PHE   0.015   0.001   PHE B  40 
 TYR   0.009   0.001   TYR A 305 
 ARG   0.006   0.001   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 (  335)
  hydrogen bonds       : angle       4.47040 (  996)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       1.09993 (   12)
  covalent geometry    : bond        0.00278 ( 7593)
  covalent geometry    : angle       0.63845 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7775 (tp30) cc_final: 0.7003 (tp30)
REVERT: A  173 PHE cc_start: 0.8541 (m-10) cc_final: 0.8028 (m-10)
REVERT: A  356 MET cc_start: 0.7968 (mmm) cc_final: 0.7571 (mmp)
REVERT: A  421 LEU cc_start: 0.8787 (tp) cc_final: 0.8584 (tp)
REVERT: A  444 MET cc_start: 0.8867 (tpp) cc_final: 0.8298 (tpp)
REVERT: B  163 MET cc_start: 0.7464 (mmm) cc_final: 0.7183 (mmm)
REVERT: B  286 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.8182 (m-10)
  outliers start: 26
  outliers final: 15
  residues processed: 188
  average time/residue: 0.1543
  time to fit residues: 40.9475
Evaluate side-chains
  175 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  416 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 62 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 8 optimal weight:    0.4980
   chunk 65 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.154249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.122511 restraints weight = 15784.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.126138 restraints weight = 8513.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.128529 restraints weight = 5666.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7599  Z= 0.108
  Angle     :  0.627  10.392  10335  Z= 0.303
  Chirality :  0.040   0.147   1250
  Planarity :  0.004   0.066   1270
  Dihedral  :  4.450  23.836   1061
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 28.52 %
    Favored  : 67.93 %
  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: -1.76 (0.26), residues: 1003
  helix: -0.13 (0.22), residues: 581
  sheet:  None (None), residues: 0
  loop : -2.72 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.010   0.001   PHE B 314 
 TYR   0.013   0.001   TYR A 354 
 ARG   0.007   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  335)
  hydrogen bonds       : angle       4.10650 (  996)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.78804 (   12)
  covalent geometry    : bond        0.00228 ( 7593)
  covalent geometry    : angle       0.62727 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ASN cc_start: 0.8263 (m110) cc_final: 0.7769 (m110)
REVERT: A  169 GLU cc_start: 0.7874 (tp30) cc_final: 0.7586 (tp30)
REVERT: A  173 PHE cc_start: 0.8586 (m-10) cc_final: 0.8308 (m-10)
REVERT: A  356 MET cc_start: 0.8015 (mmm) cc_final: 0.7746 (mmp)
REVERT: A  418 LEU cc_start: 0.8292 (mm) cc_final: 0.7952 (tt)
REVERT: A  444 MET cc_start: 0.8780 (tpp) cc_final: 0.8187 (tpp)
REVERT: B   14 MET cc_start: 0.8342 (mpp) cc_final: 0.7890 (mpp)
REVERT: B  163 MET cc_start: 0.7395 (mmm) cc_final: 0.7096 (mmm)
REVERT: B  286 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.7953 (m-10)
REVERT: B  456 ILE cc_start: 0.8947 (mp) cc_final: 0.8674 (mm)
REVERT: B  478 TYR cc_start: 0.8894 (t80) cc_final: 0.7963 (m-80)
  outliers start: 28
  outliers final: 14
  residues processed: 190
  average time/residue: 0.1554
  time to fit residues: 41.6582
Evaluate side-chains
  170 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 8 optimal weight:    0.3980
   chunk 17 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0270
   overall best weight:    0.6640

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.152675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.120237 restraints weight = 15784.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.123878 restraints weight = 8584.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.126223 restraints weight = 5754.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7599  Z= 0.109
  Angle     :  0.629  11.043  10335  Z= 0.299
  Chirality :  0.040   0.137   1250
  Planarity :  0.004   0.053   1270
  Dihedral  :  4.362  20.525   1061
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 27.88 %
    Favored  : 67.93 %
  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: -1.47 (0.26), residues: 1003
  helix:  0.15 (0.22), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.65 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.011   0.001   PHE B  40 
 TYR   0.013   0.001   TYR B 143 
 ARG   0.010   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03258 (  335)
  hydrogen bonds       : angle       3.98197 (  996)
  SS BOND              : bond        0.00142 (    6)
  SS BOND              : angle       0.89695 (   12)
  covalent geometry    : bond        0.00244 ( 7593)
  covalent geometry    : angle       0.62874 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8085 (tt)
REVERT: A  356 MET cc_start: 0.8181 (mmm) cc_final: 0.7907 (mmp)
REVERT: A  358 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8164 (mp0)
REVERT: A  418 LEU cc_start: 0.8252 (mm) cc_final: 0.7818 (tt)
REVERT: A  444 MET cc_start: 0.8808 (tpp) cc_final: 0.8350 (tpp)
REVERT: B  134 LEU cc_start: 0.6871 (mp) cc_final: 0.6476 (mt)
REVERT: B  163 MET cc_start: 0.7386 (mmm) cc_final: 0.7126 (mmm)
REVERT: B  286 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.7990 (m-10)
  outliers start: 33
  outliers final: 21
  residues processed: 192
  average time/residue: 0.1583
  time to fit residues: 42.5967
Evaluate side-chains
  180 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN
B 315 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.146772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.114134 restraints weight = 15623.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.117568 restraints weight = 8574.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.119793 restraints weight = 5793.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7599  Z= 0.143
  Angle     :  0.669  11.327  10335  Z= 0.322
  Chirality :  0.042   0.183   1250
  Planarity :  0.004   0.052   1270
  Dihedral  :  4.575  20.818   1061
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 26.36 %
    Favored  : 67.93 %
  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: -1.46 (0.26), residues: 1003
  helix:  0.14 (0.22), residues: 588
  sheet: -3.14 (1.61), residues: 10
  loop : -2.65 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B  17 
 PHE   0.012   0.001   PHE A 308 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.005   0.001   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03486 (  335)
  hydrogen bonds       : angle       4.05516 (  996)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       1.47283 (   12)
  covalent geometry    : bond        0.00324 ( 7593)
  covalent geometry    : angle       0.66726 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 TYR cc_start: 0.8151 (t80) cc_final: 0.7875 (t80)
REVERT: A  169 GLU cc_start: 0.8390 (tp30) cc_final: 0.7776 (tp30)
REVERT: A  335 TRP cc_start: 0.7705 (m-10) cc_final: 0.7049 (m-90)
REVERT: A  356 MET cc_start: 0.8436 (mmm) cc_final: 0.8088 (mmp)
REVERT: A  358 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8214 (mp0)
REVERT: A  444 MET cc_start: 0.8906 (tpp) cc_final: 0.8435 (tpp)
REVERT: B  163 MET cc_start: 0.7292 (mmm) cc_final: 0.6988 (mmm)
REVERT: B  179 LEU cc_start: 0.8010 (pt) cc_final: 0.6897 (tp)
REVERT: B  267 MET cc_start: 0.8786 (mmm) cc_final: 0.8494 (mmm)
REVERT: B  286 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.8467 (m-10)
REVERT: B  462 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8773 (tptm)
REVERT: B  478 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7718 (m-80)
  outliers start: 45
  outliers final: 29
  residues processed: 196
  average time/residue: 0.1608
  time to fit residues: 44.3514
Evaluate side-chains
  191 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 56 optimal weight:    0.1980
   chunk 29 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0670
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.150418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.117701 restraints weight = 15752.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.121215 restraints weight = 8612.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.123510 restraints weight = 5811.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7599  Z= 0.104
  Angle     :  0.651  11.040  10335  Z= 0.304
  Chirality :  0.041   0.165   1250
  Planarity :  0.004   0.045   1270
  Dihedral  :  4.379  19.835   1061
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 28.64 %
    Favored  : 67.93 %
  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: -1.23 (0.26), residues: 1003
  helix:  0.35 (0.22), residues: 586
  sheet:  None (None), residues: 0
  loop : -2.61 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.025   0.001   PHE A 173 
 TYR   0.014   0.001   TYR B 143 
 ARG   0.005   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03014 (  335)
  hydrogen bonds       : angle       3.82943 (  996)
  SS BOND              : bond        0.00249 (    6)
  SS BOND              : angle       0.83260 (   12)
  covalent geometry    : bond        0.00228 ( 7593)
  covalent geometry    : angle       0.65059 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 ASN cc_start: 0.8416 (m110) cc_final: 0.7915 (m110)
REVERT: A  159 TYR cc_start: 0.8169 (t80) cc_final: 0.7801 (t80)
REVERT: A  335 TRP cc_start: 0.7701 (m-10) cc_final: 0.7048 (m-90)
REVERT: A  356 MET cc_start: 0.8251 (mmm) cc_final: 0.7925 (mmp)
REVERT: A  358 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8120 (mp0)
REVERT: A  444 MET cc_start: 0.8759 (tpp) cc_final: 0.8235 (tpp)
REVERT: B   20 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8934 (m-30)
REVERT: B  141 ASN cc_start: 0.8790 (m110) cc_final: 0.8498 (m-40)
REVERT: B  163 MET cc_start: 0.7380 (mmm) cc_final: 0.7102 (mmm)
REVERT: B  267 MET cc_start: 0.8741 (mmm) cc_final: 0.8441 (mmm)
REVERT: B  449 MET cc_start: 0.7946 (ttm) cc_final: 0.7670 (ttp)
REVERT: B  462 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8731 (tptm)
  outliers start: 27
  outliers final: 20
  residues processed: 194
  average time/residue: 0.1504
  time to fit residues: 41.2219
Evaluate side-chains
  184 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 6 optimal weight:    0.4980
   chunk 20 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.149341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.116668 restraints weight = 15745.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.120184 restraints weight = 8639.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.122446 restraints weight = 5824.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7599  Z= 0.113
  Angle     :  0.659  12.282  10335  Z= 0.311
  Chirality :  0.042   0.178   1250
  Planarity :  0.004   0.043   1270
  Dihedral  :  4.372  20.752   1061
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 28.52 %
    Favored  : 67.93 %
  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: -1.21 (0.27), residues: 1003
  helix:  0.37 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.65 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 HIS   0.006   0.001   HIS B  17 
 PHE   0.025   0.001   PHE A 173 
 TYR   0.011   0.001   TYR A 343 
 ARG   0.004   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03151 (  335)
  hydrogen bonds       : angle       3.82964 (  996)
  SS BOND              : bond        0.00193 (    6)
  SS BOND              : angle       1.56070 (   12)
  covalent geometry    : bond        0.00257 ( 7593)
  covalent geometry    : angle       0.65751 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.5019 (t80)
REVERT: A  159 TYR cc_start: 0.8274 (t80) cc_final: 0.8065 (t80)
REVERT: A  335 TRP cc_start: 0.7731 (m-10) cc_final: 0.7114 (m-90)
REVERT: A  356 MET cc_start: 0.8309 (mmm) cc_final: 0.7963 (mmp)
REVERT: A  358 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8231 (mp0)
REVERT: A  444 MET cc_start: 0.8801 (tpp) cc_final: 0.8365 (tpp)
REVERT: B  141 ASN cc_start: 0.8641 (m110) cc_final: 0.8289 (m110)
REVERT: B  163 MET cc_start: 0.7351 (mmm) cc_final: 0.7003 (mmm)
REVERT: B  267 MET cc_start: 0.8757 (mmm) cc_final: 0.8493 (mmm)
  outliers start: 28
  outliers final: 23
  residues processed: 181
  average time/residue: 0.1559
  time to fit residues: 40.2488
Evaluate side-chains
  181 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0770
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.149552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.116644 restraints weight = 15920.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.120158 restraints weight = 8691.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.122453 restraints weight = 5874.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7599  Z= 0.112
  Angle     :  0.668  12.485  10335  Z= 0.315
  Chirality :  0.042   0.205   1250
  Planarity :  0.004   0.041   1270
  Dihedral  :  4.335  22.477   1061
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 28.01 %
    Favored  : 67.93 %
  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: -1.14 (0.27), residues: 1003
  helix:  0.42 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.62 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B  17 
 PHE   0.025   0.001   PHE B 132 
 TYR   0.016   0.001   TYR B 143 
 ARG   0.004   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  335)
  hydrogen bonds       : angle       3.84617 (  996)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.81121 (   12)
  covalent geometry    : bond        0.00252 ( 7593)
  covalent geometry    : angle       0.66757 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 TRP cc_start: 0.7742 (m-10) cc_final: 0.7132 (m-90)
REVERT: A  356 MET cc_start: 0.8403 (mmm) cc_final: 0.8062 (mmp)
REVERT: A  358 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8155 (mp0)
REVERT: A  444 MET cc_start: 0.8790 (tpp) cc_final: 0.8464 (tpp)
REVERT: A  449 MET cc_start: 0.8143 (mmt) cc_final: 0.7921 (mmt)
REVERT: B   36 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7517 (mtt180)
REVERT: B  267 MET cc_start: 0.8812 (mmm) cc_final: 0.8561 (mmm)
REVERT: B  478 TYR cc_start: 0.8919 (t80) cc_final: 0.8418 (m-80)
  outliers start: 32
  outliers final: 27
  residues processed: 185
  average time/residue: 0.1546
  time to fit residues: 41.0287
Evaluate side-chains
  184 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0020
   chunk 86 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 12 optimal weight:    0.2980
   chunk 69 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.151135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.118739 restraints weight = 15724.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.122246 restraints weight = 8576.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.124559 restraints weight = 5763.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7599  Z= 0.108
  Angle     :  0.677  12.898  10335  Z= 0.316
  Chirality :  0.042   0.237   1250
  Planarity :  0.004   0.040   1270
  Dihedral  :  4.284  25.020   1061
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 29.15 %
    Favored  : 67.55 %
  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: -1.14 (0.27), residues: 1003
  helix:  0.44 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.69 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.023   0.001   PHE B 132 
 TYR   0.015   0.001   TYR B 143 
 ARG   0.004   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03025 (  335)
  hydrogen bonds       : angle       3.79297 (  996)
  SS BOND              : bond        0.00153 (    6)
  SS BOND              : angle       1.40972 (   12)
  covalent geometry    : bond        0.00242 ( 7593)
  covalent geometry    : angle       0.67536 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5021 (t80)
REVERT: A  335 TRP cc_start: 0.7766 (m-10) cc_final: 0.7177 (m-90)
REVERT: A  356 MET cc_start: 0.8423 (mmm) cc_final: 0.8184 (mmp)
REVERT: A  358 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7987 (mp0)
REVERT: A  444 MET cc_start: 0.8745 (tpp) cc_final: 0.8423 (tpp)
REVERT: A  449 MET cc_start: 0.8082 (mmt) cc_final: 0.7881 (mmt)
REVERT: B   36 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7349 (mtt180)
REVERT: B  124 MET cc_start: 0.8315 (tpp) cc_final: 0.8090 (tpt)
REVERT: B  181 LEU cc_start: 0.8681 (pt) cc_final: 0.8458 (pp)
REVERT: B  229 LEU cc_start: 0.8501 (tt) cc_final: 0.8289 (tt)
REVERT: B  267 MET cc_start: 0.8812 (mmm) cc_final: 0.8549 (mmm)
REVERT: B  478 TYR cc_start: 0.8803 (t80) cc_final: 0.8348 (m-80)
  outliers start: 26
  outliers final: 23
  residues processed: 182
  average time/residue: 0.1477
  time to fit residues: 38.5510
Evaluate side-chains
  189 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0170
   chunk 12 optimal weight:    0.0970
   overall best weight:    0.4216

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.151622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.118649 restraints weight = 16045.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122145 restraints weight = 8692.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.124467 restraints weight = 5854.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7599  Z= 0.110
  Angle     :  0.690  13.030  10335  Z= 0.322
  Chirality :  0.042   0.291   1250
  Planarity :  0.004   0.062   1270
  Dihedral  :  4.266  25.363   1061
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 28.90 %
    Favored  : 67.81 %
  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: -1.07 (0.27), residues: 1003
  helix:  0.46 (0.22), residues: 599
  sheet:  None (None), residues: 0
  loop : -2.58 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.025   0.001   PHE B 132 
 TYR   0.020   0.001   TYR A 159 
 ARG   0.008   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03024 (  335)
  hydrogen bonds       : angle       3.80341 (  996)
  SS BOND              : bond        0.00161 (    6)
  SS BOND              : angle       1.23542 (   12)
  covalent geometry    : bond        0.00247 ( 7593)
  covalent geometry    : angle       0.68935 (10323)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.5247 (t80)
REVERT: A  181 LEU cc_start: 0.8863 (pp) cc_final: 0.8437 (mt)
REVERT: A  335 TRP cc_start: 0.7778 (m-10) cc_final: 0.7200 (m-90)
REVERT: A  341 LEU cc_start: 0.8093 (pp) cc_final: 0.7866 (pp)
REVERT: A  356 MET cc_start: 0.8408 (mmm) cc_final: 0.8166 (mmp)
REVERT: A  358 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7983 (mp0)
REVERT: A  444 MET cc_start: 0.8693 (tpp) cc_final: 0.8376 (tpp)
REVERT: B   36 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7256 (mtt180)
REVERT: B  124 MET cc_start: 0.8324 (tpp) cc_final: 0.7908 (tpt)
REVERT: B  163 MET cc_start: 0.6158 (mmm) cc_final: 0.5732 (mmt)
REVERT: B  251 THR cc_start: 0.8919 (p) cc_final: 0.8418 (t)
REVERT: B  267 MET cc_start: 0.8765 (mmm) cc_final: 0.8478 (mmm)
  outliers start: 26
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1397
  time to fit residues: 39.1964
Evaluate side-chains
  200 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0060
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.7396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.149386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.116747 restraints weight = 15777.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.120225 restraints weight = 8536.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.122439 restraints weight = 5722.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7599  Z= 0.119
  Angle     :  0.709  12.837  10335  Z= 0.330
  Chirality :  0.043   0.322   1250
  Planarity :  0.004   0.052   1270
  Dihedral  :  4.317  25.418   1061
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 29.91 %
    Favored  : 66.67 %
  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: -1.04 (0.27), residues: 1003
  helix:  0.50 (0.22), residues: 597
  sheet:  None (None), residues: 0
  loop : -2.58 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  11 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.027   0.001   PHE B 132 
 TYR   0.028   0.001   TYR A 159 
 ARG   0.007   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  335)
  hydrogen bonds       : angle       3.88521 (  996)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       1.53355 (   12)
  covalent geometry    : bond        0.00277 ( 7593)
  covalent geometry    : angle       0.70742 (10323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2613.53 seconds
wall clock time: 46 minutes 30.89 seconds (2790.89 seconds total)