Starting phenix.real_space_refine
on Fri Feb 14 09:51:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mpb_9188/02_2025/6mpb_9188.cif"
  }
  resolution = 3.84
  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=   0.027 sd=   0.326
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      48      5.16       5
     C    6498      2.51       5
     N    1656      2.21       5
     O    1767      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9969
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 3299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3299
          Classifications: {'peptide': 446}
          Link IDs: {'PTRANS': 17, 'TRANS': 428}
    Chain: "C"
      Number of atoms: 3299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3299
          Classifications: {'peptide': 446}
          Link IDs: {'PTRANS': 17, 'TRANS': 428}
    Chain: "A"
      Number of atoms: 3299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3299
          Classifications: {'peptide': 446}
          Link IDs: {'PTRANS': 17, 'TRANS': 428}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.71, per 1000 atoms: 0.57
  Number of scatterers: 9969
  At special positions: 0
  Unit cell: (121.632, 111.858, 119.46, 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      48     16.00
     O    1767      8.00
     N    1656      7.00
     C    6498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Links applied
    NAG-ASN
      " NAG B 602 " - " ASN B 163 "
      " NAG C 602 " - " ASN C 163 "
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2424

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 3 sheets defined
      76.3% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'B' and resid 44 through 52
      removed outlier: 3.827A  pdb=" N   CYS B  48 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B  49 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 75
      removed outlier: 3.568A  pdb=" N   VAL B  59 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.510A  pdb=" N   LEU B  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 100
      removed outlier: 3.852A  pdb=" N   SER B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ALA B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
      removed outlier: 3.922A  pdb=" N   LEU B  96 " --> pdb=" O   PRO B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 116
      removed outlier: 3.846A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   CYS B 110 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ILE B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLY B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 151
      removed outlier: 3.673A  pdb=" N   ARG B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TRP B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
      removed outlier: 3.602A  pdb=" N   ILE B 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 169
      removed outlier: 3.896A  pdb=" N   ALA B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
      removed outlier: 3.786A  pdb=" N   ALA B 188 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 201
      removed outlier: 3.862A  pdb=" N   PHE B 201 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 248
      removed outlier: 3.801A  pdb=" N   LEU B 234 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU B 245 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 292
      removed outlier: 4.426A  pdb=" N   LEU B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG B 257 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TRP B 272 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TRP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR B 276 " --> pdb=" O   TRP B 272 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.941A  pdb=" N   MET B 282 " --> pdb=" O   PRO B 278 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE B 283 " --> pdb=" O   VAL B 279 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA B 286 " --> pdb=" O   MET B 282 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   VAL B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLU B 291 " --> pdb=" O   GLY B 287 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   MET B 292 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 316
      removed outlier: 3.570A  pdb=" N   ARG B 301 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LYS B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TYR B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 330
      removed outlier: 3.566A  pdb=" N   LEU B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.593A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 351
    Processing helix  chain 'B' and resid 356 through 367
      removed outlier: 3.945A  pdb=" N   GLU B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 382
      removed outlier: 3.612A  pdb=" N   SER B 375 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE B 377 " --> pdb=" O   HIS B 373 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU B 379 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      Proline residue:  B 380  - end of helix
    Processing helix  chain 'B' and resid 387 through 404
      removed outlier: 3.802A  pdb=" N   CYS B 395 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ALA B 402 " --> pdb=" O   ALA B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 428
      removed outlier: 3.687A  pdb=" N   ILE B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   VAL B 426 " --> pdb=" O   THR B 422 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B 427 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 439 through 446
      removed outlier: 3.663A  pdb=" N   ALA B 445 " --> pdb=" O   ILE B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 488
      removed outlier: 3.616A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY B 474 " --> pdb=" O   LEU B 470 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN B 483 " --> pdb=" O   ALA B 479 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR B 485 " --> pdb=" O   LEU B 481 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG B 488 " --> pdb=" O   ASN B 484 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 52
      removed outlier: 3.827A  pdb=" N   CYS C  48 " --> pdb=" O   GLN C  44 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU C  49 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 75
      removed outlier: 3.568A  pdb=" N   VAL C  59 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL C  63 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL C  66 " --> pdb=" O   VAL C  62 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 81
      removed outlier: 3.509A  pdb=" N   LEU C  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 100
      removed outlier: 3.854A  pdb=" N   SER C  87 " --> pdb=" O   PRO C  83 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ALA C  88 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      Proline residue:  C  92  - end of helix
      removed outlier: 3.922A  pdb=" N   LEU C  96 " --> pdb=" O   PRO C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 116
      removed outlier: 3.847A  pdb=" N   VAL C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   CYS C 110 " --> pdb=" O   PRO C 106 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU C 112 " --> pdb=" O   VAL C 108 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ILE C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY C 114 " --> pdb=" O   CYS C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 151
      removed outlier: 3.673A  pdb=" N   ARG C 126 " --> pdb=" O   GLY C 122 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TRP C 130 " --> pdb=" O   ARG C 126 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL C 147 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 3.602A  pdb=" N   ILE C 162 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 169
      removed outlier: 3.896A  pdb=" N   ALA C 169 " --> pdb=" O   SER C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 191
      removed outlier: 3.785A  pdb=" N   ALA C 188 " --> pdb=" O   PHE C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 201
      removed outlier: 3.861A  pdb=" N   PHE C 201 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 248
      removed outlier: 3.802A  pdb=" N   LEU C 234 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL C 240 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C 245 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG C 246 " --> pdb=" O   GLY C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 292
      removed outlier: 4.426A  pdb=" N   LEU C 255 " --> pdb=" O   GLU C 251 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR C 266 " --> pdb=" O   PHE C 262 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER C 271 " --> pdb=" O   MET C 267 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TRP C 272 " --> pdb=" O   VAL C 268 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE C 273 " --> pdb=" O   LEU C 269 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TRP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR C 276 " --> pdb=" O   TRP C 272 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
      removed outlier: 3.940A  pdb=" N   MET C 282 " --> pdb=" O   PRO C 278 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE C 283 " --> pdb=" O   VAL C 279 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA C 286 " --> pdb=" O   MET C 282 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   VAL C 290 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   MET C 292 " --> pdb=" O   LYS C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 316
      removed outlier: 3.570A  pdb=" N   ARG C 301 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU C 302 " --> pdb=" O   LEU C 298 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LYS C 304 " --> pdb=" O   ALA C 300 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TYR C 305 " --> pdb=" O   ARG C 301 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   HIS C 316 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 330
      removed outlier: 3.565A  pdb=" N   LEU C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 339
      removed outlier: 3.592A  pdb=" N   PHE C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY C 339 " --> pdb=" O   ARG C 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 351
    Processing helix  chain 'C' and resid 356 through 367
      removed outlier: 3.945A  pdb=" N   GLU C 365 " --> pdb=" O   MET C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 382
      removed outlier: 3.613A  pdb=" N   SER C 375 " --> pdb=" O   ALA C 371 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ARG C 376 " --> pdb=" O   LYS C 372 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE C 377 " --> pdb=" O   HIS C 373 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU C 379 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      Proline residue:  C 380  - end of helix
    Processing helix  chain 'C' and resid 387 through 404
      removed outlier: 3.801A  pdb=" N   CYS C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA C 398 " --> pdb=" O   GLN C 394 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE C 401 " --> pdb=" O   ALA C 397 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ALA C 402 " --> pdb=" O   ALA C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 428
      removed outlier: 3.688A  pdb=" N   ILE C 415 " --> pdb=" O   PHE C 411 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR C 416 " --> pdb=" O   VAL C 412 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR C 422 " --> pdb=" O   LEU C 418 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   VAL C 426 " --> pdb=" O   THR C 422 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY C 427 " --> pdb=" O   ALA C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 436 through 438
      No H-bonds generated for 'chain 'C' and resid 436 through 438'
    Processing helix  chain 'C' and resid 439 through 446
      removed outlier: 3.663A  pdb=" N   ALA C 445 " --> pdb=" O   ILE C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 488
      removed outlier: 3.615A  pdb=" N   SER C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL C 469 " --> pdb=" O   ARG C 465 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY C 474 " --> pdb=" O   LEU C 470 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA C 476 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN C 483 " --> pdb=" O   ALA C 479 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN C 484 " --> pdb=" O   GLY C 480 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR C 485 " --> pdb=" O   LEU C 481 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASP C 487 " --> pdb=" O   GLN C 483 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG C 488 " --> pdb=" O   ASN C 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 52
      removed outlier: 3.827A  pdb=" N   CYS A  48 " --> pdb=" O   GLN A  44 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 75
      removed outlier: 3.568A  pdb=" N   VAL A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 81
      removed outlier: 3.510A  pdb=" N   LEU A  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 100
      removed outlier: 3.852A  pdb=" N   SER A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ALA A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
      removed outlier: 3.922A  pdb=" N   LEU A  96 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
      removed outlier: 3.847A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   CYS A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ILE A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLY A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 151
      removed outlier: 3.673A  pdb=" N   ARG A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TRP A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 163
      removed outlier: 3.602A  pdb=" N   ILE A 162 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 169
      removed outlier: 3.896A  pdb=" N   ALA A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 3.786A  pdb=" N   ALA A 188 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 201
      removed outlier: 3.861A  pdb=" N   PHE A 201 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 248
      removed outlier: 3.800A  pdb=" N   LEU A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 292
      removed outlier: 4.426A  pdb=" N   LEU A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TRP A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TRP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR A 276 " --> pdb=" O   TRP A 272 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
      removed outlier: 3.940A  pdb=" N   MET A 282 " --> pdb=" O   PRO A 278 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 286 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   VAL A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLU A 291 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   MET A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 316
      removed outlier: 3.569A  pdb=" N   ARG A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LYS A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TYR A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 330
      removed outlier: 3.564A  pdb=" N   LEU A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 339
      removed outlier: 3.592A  pdb=" N   PHE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLY A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 351
    Processing helix  chain 'A' and resid 356 through 367
      removed outlier: 3.945A  pdb=" N   GLU A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 382
      removed outlier: 3.613A  pdb=" N   SER A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ARG A 376 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 377 " --> pdb=" O   HIS A 373 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 387 through 404
      removed outlier: 3.801A  pdb=" N   CYS A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ALA A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 428
      removed outlier: 3.688A  pdb=" N   ILE A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   VAL A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 438
      No H-bonds generated for 'chain 'A' and resid 436 through 438'
    Processing helix  chain 'A' and resid 439 through 446
      removed outlier: 3.663A  pdb=" N   ALA A 445 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 488
      removed outlier: 3.616A  pdb=" N   SER A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ASP A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA A 476 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG A 488 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 207 through 209
    Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 209
    Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209

    519 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3149
        1.34 -     1.46: 1456
        1.46 -     1.57: 5463
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 10143
  Sorted by residual:
  bond pdb=" C1  NAG B 602 "
       pdb=" O5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.96e+00
  bond pdb=" C1  NAG C 602 "
       pdb=" O5  NAG C 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.65e+00
  bond pdb=" C   LEU C 105 "
       pdb=" N   PRO C 106 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.45e+00
  bond pdb=" N   ASN C 447 "
       pdb=" CA  ASN C 447 "
    ideal  model  delta    sigma   weight residual
    1.460  1.484 -0.024 1.54e-02 4.22e+03 2.42e+00
  ... (remaining 10138 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 13504
        3.11 -     6.23: 239
        6.23 -     9.34: 72
        9.34 -    12.46: 0
       12.46 -    15.57: 6
  Bond angle restraints: 13821
  Sorted by residual:
  angle pdb=" C   VAL B 446 "
        pdb=" N   ASN B 447 "
        pdb=" CA  ASN B 447 "
      ideal   model   delta    sigma   weight residual
     122.46  129.79   -7.33 1.41e+00 5.03e-01 2.70e+01
  angle pdb=" C   VAL C 446 "
        pdb=" N   ASN C 447 "
        pdb=" CA  ASN C 447 "
      ideal   model   delta    sigma   weight residual
     122.46  129.77   -7.31 1.41e+00 5.03e-01 2.69e+01
  angle pdb=" C   VAL A 446 "
        pdb=" N   ASN A 447 "
        pdb=" CA  ASN A 447 "
      ideal   model   delta    sigma   weight residual
     122.46  129.73   -7.27 1.41e+00 5.03e-01 2.66e+01
  angle pdb=" CA  LEU C 409 "
        pdb=" CB  LEU C 409 "
        pdb=" CG  LEU C 409 "
      ideal   model   delta    sigma   weight residual
     116.30  131.87  -15.57 3.50e+00 8.16e-02 1.98e+01
  angle pdb=" CA  LEU B 409 "
        pdb=" CB  LEU B 409 "
        pdb=" CG  LEU B 409 "
      ideal   model   delta    sigma   weight residual
     116.30  131.84  -15.54 3.50e+00 8.16e-02 1.97e+01
  ... (remaining 13816 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.01: 5600
       15.01 -    30.01: 330
       30.01 -    45.01: 70
       45.01 -    60.02: 5
       60.02 -    75.02: 7
  Dihedral angle restraints: 6012
    sinusoidal: 2232
      harmonic: 3780
  Sorted by residual:
  dihedral pdb=" CA  ARG B 211 "
           pdb=" C   ARG B 211 "
           pdb=" N   ASN B 212 "
           pdb=" CA  ASN B 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.05  -21.95     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ARG A 211 "
           pdb=" C   ARG A 211 "
           pdb=" N   ASN A 212 "
           pdb=" CA  ASN A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.06  -21.94     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ARG C 211 "
           pdb=" C   ARG C 211 "
           pdb=" N   ASN C 212 "
           pdb=" CA  ASN C 212 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.09  -21.91     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 6009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1332
       0.062 -    0.123: 322
       0.123 -    0.185: 65
       0.185 -    0.246: 3
       0.246 -    0.307: 8
  Chirality restraints: 1730
  Sorted by residual:
  chirality pdb=" CB  VAL A 446 "
            pdb=" CA  VAL A 446 "
            pdb=" CG1 VAL A 446 "
            pdb=" CG2 VAL A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CB  VAL B 446 "
            pdb=" CA  VAL B 446 "
            pdb=" CG1 VAL B 446 "
            pdb=" CG2 VAL B 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CB  VAL C 446 "
            pdb=" CA  VAL C 446 "
            pdb=" CG1 VAL C 446 "
            pdb=" CG2 VAL C 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.30 2.00e-01 2.50e+01 2.32e+00
  ... (remaining 1727 not shown)

  Planarity restraints: 1727
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 211 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.34e+00
        pdb=" C   ARG C 211 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ARG C 211 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN C 212 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 211 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   ARG B 211 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG B 211 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN B 212 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 211 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.16e+00
        pdb=" C   ARG A 211 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG A 211 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 212 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1724 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3232
        2.85 -     3.36: 10038
        3.36 -     3.88: 15549
        3.88 -     4.39: 17580
        4.39 -     4.90: 29128
  Nonbonded interactions: 75527
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 352 "
            pdb=" O   GLY A 430 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OG  SER C 352 "
            pdb=" O   GLY C 430 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG  SER B 352 "
            pdb=" O   GLY B 430 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NE2 GLN C 394 "
            pdb=" OG1 THR C 438 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" NE2 GLN B 394 "
            pdb=" OG1 THR B 438 "
     model   vdw
     2.378 3.120
  ... (remaining 75522 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.990
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
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      :  0.005   0.059  10143  Z= 0.323
  Angle     :  1.087  15.570  13821  Z= 0.510
  Chirality :  0.058   0.307   1730
  Planarity :  0.006   0.049   1725
  Dihedral  : 10.552  75.024   3588
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.64 %
    Favored  : 87.36 %
  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: -5.90 (0.15), residues: 1332
  helix: -4.15 (0.09), residues: 846
  sheet:  None (None), residues: 0
  loop : -3.10 (0.23), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 272 
 HIS   0.004   0.001   HIS C 316 
 PHE   0.015   0.001   PHE C 201 
 TYR   0.008   0.002   TYR C 334 
 ARG   0.004   0.001   ARG C 217 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 412
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  207 THR cc_start: 0.9006 (p) cc_final: 0.8736 (p)
REVERT: B  307 LEU cc_start: 0.9225 (tm) cc_final: 0.8724 (mt)
REVERT: B  311 LEU cc_start: 0.9256 (tp) cc_final: 0.9013 (tp)
REVERT: B  318 LEU cc_start: 0.9328 (tm) cc_final: 0.9107 (mm)
REVERT: B  394 GLN cc_start: 0.8394 (mt0) cc_final: 0.8192 (mt0)
REVERT: B  403 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8611 (mm-40)
REVERT: C  149 LEU cc_start: 0.9002 (tm) cc_final: 0.8758 (tm)
REVERT: C  210 GLU cc_start: 0.5826 (mp0) cc_final: 0.5496 (mm-30)
REVERT: C  253 GLU cc_start: 0.7631 (tp30) cc_final: 0.7295 (tp30)
REVERT: C  267 MET cc_start: 0.8461 (tpp) cc_final: 0.7502 (tpp)
REVERT: C  313 HIS cc_start: 0.8809 (m90) cc_final: 0.8422 (m-70)
REVERT: C  353 SER cc_start: 0.9010 (t) cc_final: 0.8686 (p)
REVERT: C  366 GLU cc_start: 0.8478 (tt0) cc_final: 0.8176 (tm-30)
REVERT: C  388 ASP cc_start: 0.8674 (p0) cc_final: 0.8216 (p0)
REVERT: C  462 LEU cc_start: 0.8976 (tp) cc_final: 0.8749 (tp)
REVERT: A  130 TRP cc_start: 0.8143 (m100) cc_final: 0.7699 (m100)
REVERT: A  184 PHE cc_start: 0.7971 (t80) cc_final: 0.7628 (m-80)
REVERT: A  264 GLU cc_start: 0.8866 (tp30) cc_final: 0.8287 (tp30)
REVERT: A  348 PHE cc_start: 0.8835 (t80) cc_final: 0.8472 (t80)
REVERT: A  363 CYS cc_start: 0.9042 (m) cc_final: 0.8665 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 412
  average time/residue: 0.2364
  time to fit residues: 134.8310
Evaluate side-chains
  218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 119 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 224 GLN
C 394 GLN
C 483 GLN
A 163 ASN
A 224 GLN
A 483 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.097299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.079044 restraints weight = 27844.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.081426 restraints weight = 14687.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.083015 restraints weight = 9513.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10143  Z= 0.203
  Angle     :  0.739  10.116  13821  Z= 0.354
  Chirality :  0.043   0.205   1730
  Planarity :  0.005   0.034   1725
  Dihedral  :  5.185  52.041   1479
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 19.35 %
    Favored  : 73.37 %
  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: -3.62 (0.19), residues: 1332
  helix: -2.07 (0.14), residues: 909
  sheet: -1.67 (0.98), residues: 30
  loop : -2.83 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 452 
 PHE   0.016   0.001   PHE A 192 
 TYR   0.018   0.001   TYR B 485 
 ARG   0.003   0.000   ARG B 465 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 262
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  141 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9135 (mm)
REVERT: B  178 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8716 (ptmm)
REVERT: B  225 GLU cc_start: 0.8776 (mp0) cc_final: 0.8464 (mp0)
REVERT: B  275 TRP cc_start: 0.8441 (m100) cc_final: 0.8160 (m-10)
REVERT: B  302 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8709 (pp)
REVERT: B  307 LEU cc_start: 0.9057 (tm) cc_final: 0.8546 (mt)
REVERT: B  311 LEU cc_start: 0.9160 (tp) cc_final: 0.8629 (mm)
REVERT: B  329 THR cc_start: 0.8055 (p) cc_final: 0.7793 (p)
REVERT: B  331 LYS cc_start: 0.8516 (mttp) cc_final: 0.8265 (mttp)
REVERT: B  387 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7936 (mmp)
REVERT: C  149 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8857 (tm)
REVERT: C  313 HIS cc_start: 0.8787 (m90) cc_final: 0.8460 (m-70)
REVERT: C  328 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8334 (t80)
REVERT: C  334 TYR cc_start: 0.8373 (m-10) cc_final: 0.7819 (t80)
REVERT: C  366 GLU cc_start: 0.8436 (tt0) cc_final: 0.8218 (tm-30)
REVERT: C  471 ASN cc_start: 0.8627 (t0) cc_final: 0.8371 (t0)
REVERT: C  481 LEU cc_start: 0.9092 (tt) cc_final: 0.8713 (mm)
REVERT: A   50 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7168 (tpt90)
REVERT: A   94 GLU cc_start: 0.8131 (tp30) cc_final: 0.7804 (tp30)
REVERT: A  130 TRP cc_start: 0.8211 (m100) cc_final: 0.7624 (m100)
REVERT: A  319 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (mp)
REVERT: A  332 ASN cc_start: 0.8462 (t0) cc_final: 0.7734 (m-40)
REVERT: A  363 CYS cc_start: 0.9114 (m) cc_final: 0.8468 (m)
REVERT: A  387 MET cc_start: 0.8010 (mmm) cc_final: 0.7718 (mmm)
REVERT: A  464 ASP cc_start: 0.8121 (t70) cc_final: 0.7912 (t70)
REVERT: A  465 ARG cc_start: 0.9090 (mmm-85) cc_final: 0.8714 (mtt-85)
  outliers start: 76
  outliers final: 32
  residues processed: 311
  average time/residue: 0.1932
  time to fit residues: 86.8488
Evaluate side-chains
  248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 209
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  219 LYS
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  438 THR
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  354 SER
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  401 ILE
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  457 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 20 optimal weight:    0.8980
   chunk 120 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 90 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** B 483 GLN ** 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 = 0.3385 r_free = 0.3385 target = 0.096067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.077510 restraints weight = 28595.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.079828 restraints weight = 15334.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.081369 restraints weight = 10060.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10143  Z= 0.195
  Angle     :  0.725  13.368  13821  Z= 0.336
  Chirality :  0.043   0.230   1730
  Planarity :  0.004   0.035   1725
  Dihedral  :  4.747  51.995   1479
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 21.55 %
    Favored  : 71.74 %
  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: -2.23 (0.22), residues: 1332
  helix: -1.01 (0.16), residues: 924
  sheet: -1.28 (1.01), residues: 30
  loop : -2.37 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 461 
 HIS   0.004   0.001   HIS C 452 
 PHE   0.014   0.001   PHE B 135 
 TYR   0.011   0.001   TYR B 305 
 ARG   0.004   0.000   ARG A  47 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 229
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  141 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9120 (mm)
REVERT: B  225 GLU cc_start: 0.8834 (mp0) cc_final: 0.8534 (mp0)
REVERT: B  275 TRP cc_start: 0.8442 (m100) cc_final: 0.8155 (m-10)
REVERT: B  282 MET cc_start: 0.8714 (ttt) cc_final: 0.8398 (ttp)
REVERT: B  302 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: B  387 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7982 (mmp)
REVERT: B  413 LYS cc_start: 0.9130 (mttp) cc_final: 0.8914 (mttm)
REVERT: B  465 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7640 (mtp85)
REVERT: C  149 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8937 (tm)
REVERT: C  313 HIS cc_start: 0.8884 (m90) cc_final: 0.8622 (m-70)
REVERT: C  328 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8321 (t80)
REVERT: C  334 TYR cc_start: 0.8191 (m-10) cc_final: 0.7835 (t80)
REVERT: A   50 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7274 (tpt90)
REVERT: A   94 GLU cc_start: 0.8308 (tp30) cc_final: 0.8080 (tp30)
REVERT: A  130 TRP cc_start: 0.8193 (m100) cc_final: 0.7666 (m100)
REVERT: A  214 THR cc_start: 0.5469 (OUTLIER) cc_final: 0.4823 (t)
REVERT: A  229 MET cc_start: 0.8323 (tmm) cc_final: 0.7993 (tmm)
REVERT: A  267 MET cc_start: 0.8789 (tpt) cc_final: 0.8501 (mmm)
REVERT: A  313 HIS cc_start: 0.8900 (m90) cc_final: 0.8650 (m90)
REVERT: A  363 CYS cc_start: 0.9224 (m) cc_final: 0.8458 (m)
REVERT: A  387 MET cc_start: 0.8055 (mmm) cc_final: 0.7370 (mmm)
REVERT: A  403 GLN cc_start: 0.9008 (tp40) cc_final: 0.8553 (tm-30)
REVERT: A  465 ARG cc_start: 0.9072 (mmm-85) cc_final: 0.8315 (mtt-85)
REVERT: A  471 ASN cc_start: 0.8702 (t0) cc_final: 0.8201 (t0)
  outliers start: 70
  outliers final: 39
  residues processed: 274
  average time/residue: 0.1901
  time to fit residues: 75.4890
Evaluate side-chains
  243 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 198
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  219 LYS
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  438 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  171 SER
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  354 SER
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  401 ILE
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  457 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 88 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 121 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN
B 403 GLN
A 316 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.079032 restraints weight = 28394.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.081329 restraints weight = 15099.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.082770 restraints weight = 9812.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10143  Z= 0.166
  Angle     :  0.698  12.901  13821  Z= 0.319
  Chirality :  0.041   0.192   1730
  Planarity :  0.004   0.035   1725
  Dihedral  :  4.485  52.061   1479
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 22.51 %
    Favored  : 70.69 %
  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: -1.48 (0.23), residues: 1332
  helix: -0.43 (0.17), residues: 936
  sheet: -1.25 (1.00), residues: 30
  loop : -2.14 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 452 
 PHE   0.014   0.001   PHE C 299 
 TYR   0.008   0.001   TYR B 305 
 ARG   0.003   0.000   ARG C  98 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 226
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (tm)
REVERT: B  141 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9112 (mm)
REVERT: B  225 GLU cc_start: 0.8798 (mp0) cc_final: 0.8526 (mp0)
REVERT: B  302 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8788 (pp)
REVERT: B  362 LYS cc_start: 0.8853 (tptt) cc_final: 0.8375 (tppt)
REVERT: B  363 CYS cc_start: 0.8930 (m) cc_final: 0.8152 (t)
REVERT: B  465 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7352 (mtp85)
REVERT: C   94 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8486 (tt0)
REVERT: C  149 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8941 (tm)
REVERT: C  313 HIS cc_start: 0.8910 (m90) cc_final: 0.8641 (m-70)
REVERT: C  334 TYR cc_start: 0.8080 (m-10) cc_final: 0.7753 (t80)
REVERT: A   50 ARG cc_start: 0.7807 (mtm180) cc_final: 0.7163 (tpt90)
REVERT: A   94 GLU cc_start: 0.8373 (tp30) cc_final: 0.8102 (tp30)
REVERT: A  130 TRP cc_start: 0.8216 (m100) cc_final: 0.7669 (m100)
REVERT: A  214 THR cc_start: 0.5669 (OUTLIER) cc_final: 0.5046 (t)
REVERT: A  229 MET cc_start: 0.8296 (tmm) cc_final: 0.8041 (tmm)
REVERT: A  267 MET cc_start: 0.8760 (tpt) cc_final: 0.8466 (mmm)
REVERT: A  302 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8614 (pp)
REVERT: A  305 TYR cc_start: 0.9034 (t80) cc_final: 0.8644 (t80)
REVERT: A  332 ASN cc_start: 0.8398 (t0) cc_final: 0.7676 (m-40)
REVERT: A  363 CYS cc_start: 0.9195 (m) cc_final: 0.8494 (m)
REVERT: A  387 MET cc_start: 0.8082 (mmm) cc_final: 0.7639 (mmm)
REVERT: A  403 GLN cc_start: 0.8988 (tp40) cc_final: 0.8548 (tm-30)
REVERT: A  465 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8326 (mtt-85)
REVERT: A  471 ASN cc_start: 0.8602 (t0) cc_final: 0.8188 (t0)
  outliers start: 71
  outliers final: 37
  residues processed: 267
  average time/residue: 0.1812
  time to fit residues: 70.9021
Evaluate side-chains
  243 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 200
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  171 SER
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  354 SER
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  401 ILE
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0370
   chunk 54 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0060
   chunk 90 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7676

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

Flipped N/Q/H residues before XYZ refinement:
B 403 GLN
A 316 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.096417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.078670 restraints weight = 28455.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.080948 restraints weight = 15143.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.082447 restraints weight = 9860.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10143  Z= 0.175
  Angle     :  0.694  12.582  13821  Z= 0.316
  Chirality :  0.042   0.266   1730
  Planarity :  0.003   0.035   1725
  Dihedral  :  4.344  51.954   1479
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 24.43 %
    Favored  : 68.87 %
  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: -1.03 (0.23), residues: 1332
  helix: -0.07 (0.17), residues: 936
  sheet: -1.20 (1.01), residues: 30
  loop : -2.05 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 452 
 PHE   0.009   0.001   PHE B 135 
 TYR   0.009   0.001   TYR B 305 
 ARG   0.002   0.000   ARG A 101 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 221
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8762 (tm)
REVERT: B  141 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9099 (mm)
REVERT: B  225 GLU cc_start: 0.8836 (mp0) cc_final: 0.8634 (mp0)
REVERT: B  302 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8777 (pp)
REVERT: B  363 CYS cc_start: 0.8835 (m) cc_final: 0.8122 (t)
REVERT: B  387 MET cc_start: 0.8157 (mmp) cc_final: 0.7660 (mmm)
REVERT: B  431 ILE cc_start: 0.8564 (mt) cc_final: 0.8272 (tt)
REVERT: B  465 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7372 (mtp85)
REVERT: C   92 PRO cc_start: 0.9396 (Cg_exo) cc_final: 0.9193 (Cg_endo)
REVERT: C  149 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8963 (tm)
REVERT: C  313 HIS cc_start: 0.9037 (m90) cc_final: 0.8184 (m-70)
REVERT: C  328 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8037 (t80)
REVERT: C  334 TYR cc_start: 0.8112 (m-10) cc_final: 0.7756 (t80)
REVERT: C  360 MET cc_start: 0.9409 (tpt) cc_final: 0.9158 (tpp)
REVERT: A   50 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7240 (tpt90)
REVERT: A   94 GLU cc_start: 0.8391 (tp30) cc_final: 0.8118 (tp30)
REVERT: A  130 TRP cc_start: 0.8320 (m100) cc_final: 0.7736 (m100)
REVERT: A  229 MET cc_start: 0.8389 (tmm) cc_final: 0.8119 (tmm)
REVERT: A  267 MET cc_start: 0.8801 (tpt) cc_final: 0.8467 (mmm)
REVERT: A  302 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8669 (pp)
REVERT: A  332 ASN cc_start: 0.8438 (t0) cc_final: 0.7701 (m-40)
REVERT: A  334 TYR cc_start: 0.7906 (m-10) cc_final: 0.7672 (m-10)
REVERT: A  359 LEU cc_start: 0.9084 (tp) cc_final: 0.8723 (tt)
REVERT: A  363 CYS cc_start: 0.9134 (m) cc_final: 0.8347 (m)
REVERT: A  366 GLU cc_start: 0.8158 (tt0) cc_final: 0.7865 (tt0)
REVERT: A  387 MET cc_start: 0.8148 (mmm) cc_final: 0.7594 (mmm)
REVERT: A  403 GLN cc_start: 0.9131 (tp40) cc_final: 0.8592 (tm-30)
REVERT: A  470 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (tm)
REVERT: A  471 ASN cc_start: 0.8620 (t0) cc_final: 0.8293 (t0)
  outliers start: 70
  outliers final: 39
  residues processed: 266
  average time/residue: 0.1863
  time to fit residues: 72.2876
Evaluate side-chains
  250 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 204
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  354 SER
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 80 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 126 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN
B 403 GLN
** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.094671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.076751 restraints weight = 28654.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.078992 restraints weight = 15167.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.080425 restraints weight = 9904.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10143  Z= 0.219
  Angle     :  0.728  12.265  13821  Z= 0.337
  Chirality :  0.043   0.223   1730
  Planarity :  0.004   0.044   1725
  Dihedral  :  4.415  51.705   1479
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 24.52 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.24), residues: 1332
  helix:  0.10 (0.17), residues: 939
  sheet: -1.22 (1.01), residues: 30
  loop : -1.89 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 461 
 HIS   0.004   0.001   HIS A 452 
 PHE   0.025   0.001   PHE B 411 
 TYR   0.010   0.001   TYR C 325 
 ARG   0.003   0.000   ARG C 376 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 210
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 MET cc_start: 0.8830 (ppp) cc_final: 0.8564 (ppp)
REVERT: B  127 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8714 (tm)
REVERT: B  141 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9110 (mm)
REVERT: B  225 GLU cc_start: 0.8854 (mp0) cc_final: 0.8578 (mp0)
REVERT: B  302 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8786 (pp)
REVERT: B  363 CYS cc_start: 0.8901 (m) cc_final: 0.8298 (t)
REVERT: B  387 MET cc_start: 0.8271 (mmp) cc_final: 0.7570 (mmm)
REVERT: B  431 ILE cc_start: 0.8574 (mt) cc_final: 0.8322 (tt)
REVERT: B  465 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7453 (mmm-85)
REVERT: C  313 HIS cc_start: 0.9067 (m90) cc_final: 0.8193 (m-70)
REVERT: C  334 TYR cc_start: 0.8176 (m-10) cc_final: 0.7740 (t80)
REVERT: C  418 LEU cc_start: 0.9270 (tt) cc_final: 0.8967 (pp)
REVERT: A   50 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7343 (tpt90)
REVERT: A   94 GLU cc_start: 0.8442 (tp30) cc_final: 0.8205 (tp30)
REVERT: A  130 TRP cc_start: 0.8304 (m100) cc_final: 0.7737 (m100)
REVERT: A  229 MET cc_start: 0.8382 (tmm) cc_final: 0.8140 (tmm)
REVERT: A  292 MET cc_start: 0.7977 (mpp) cc_final: 0.7498 (mmm)
REVERT: A  359 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8755 (tp)
REVERT: A  363 CYS cc_start: 0.9217 (m) cc_final: 0.8447 (m)
REVERT: A  366 GLU cc_start: 0.8192 (tt0) cc_final: 0.7948 (tt0)
REVERT: A  403 GLN cc_start: 0.9197 (tp40) cc_final: 0.8620 (tm-30)
REVERT: A  470 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8468 (tm)
  outliers start: 74
  outliers final: 48
  residues processed: 257
  average time/residue: 0.1824
  time to fit residues: 69.1559
Evaluate side-chains
  249 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 196
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  308 CYS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  354 SER
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  472 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0770
   chunk 84 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0070
   chunk 3 optimal weight:    8.9990
   chunk 125 optimal weight:    0.7980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN
B 403 GLN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.096803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.078969 restraints weight = 28861.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.081288 restraints weight = 15220.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.082808 restraints weight = 9842.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.5612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10143  Z= 0.171
  Angle     :  0.731  12.352  13821  Z= 0.330
  Chirality :  0.042   0.198   1730
  Planarity :  0.004   0.044   1725
  Dihedral  :  4.295  52.266   1479
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 26.53 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.24), residues: 1332
  helix:  0.32 (0.17), residues: 930
  sheet: -1.20 (1.00), residues: 30
  loop : -1.83 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 461 
 HIS   0.005   0.001   HIS C 452 
 PHE   0.012   0.001   PHE A 134 
 TYR   0.009   0.001   TYR C 325 
 ARG   0.003   0.000   ARG B 246 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 219
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 MET cc_start: 0.8772 (ppp) cc_final: 0.8499 (ppp)
REVERT: B  127 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8589 (tm)
REVERT: B  141 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9090 (mm)
REVERT: B  225 GLU cc_start: 0.8851 (mp0) cc_final: 0.8617 (mp0)
REVERT: B  282 MET cc_start: 0.8400 (ttt) cc_final: 0.8153 (ttp)
REVERT: B  283 PHE cc_start: 0.9215 (m-80) cc_final: 0.8998 (m-80)
REVERT: B  302 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (pp)
REVERT: B  363 CYS cc_start: 0.8812 (m) cc_final: 0.8249 (t)
REVERT: B  387 MET cc_start: 0.8098 (mmp) cc_final: 0.7868 (mmp)
REVERT: B  394 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7838 (tt0)
REVERT: B  431 ILE cc_start: 0.8601 (mt) cc_final: 0.8367 (tt)
REVERT: B  465 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7480 (mtp85)
REVERT: C  186 ASP cc_start: 0.8657 (t70) cc_final: 0.7991 (t0)
REVERT: C  313 HIS cc_start: 0.8982 (m90) cc_final: 0.8060 (m-70)
REVERT: C  328 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8053 (t80)
REVERT: C  334 TYR cc_start: 0.8034 (m-10) cc_final: 0.7635 (t80)
REVERT: C  408 SER cc_start: 0.7025 (m) cc_final: 0.6686 (t)
REVERT: C  418 LEU cc_start: 0.9272 (tt) cc_final: 0.9018 (pp)
REVERT: A   50 ARG cc_start: 0.7838 (mtm180) cc_final: 0.7318 (tpt90)
REVERT: A   94 GLU cc_start: 0.8452 (tp30) cc_final: 0.8181 (tp30)
REVERT: A  229 MET cc_start: 0.8373 (tmm) cc_final: 0.7890 (tmm)
REVERT: A  267 MET cc_start: 0.8779 (tpt) cc_final: 0.8453 (mmm)
REVERT: A  292 MET cc_start: 0.7917 (mpp) cc_final: 0.7500 (mmm)
REVERT: A  302 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8578 (pp)
REVERT: A  305 TYR cc_start: 0.9083 (t80) cc_final: 0.8877 (t80)
REVERT: A  307 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8716 (tp)
REVERT: A  332 ASN cc_start: 0.8350 (t0) cc_final: 0.7642 (m-40)
REVERT: A  359 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8829 (tt)
REVERT: A  363 CYS cc_start: 0.9170 (m) cc_final: 0.8278 (m)
REVERT: A  403 GLN cc_start: 0.9125 (tp40) cc_final: 0.8606 (tm-30)
REVERT: A  418 LEU cc_start: 0.9219 (mt) cc_final: 0.8661 (mt)
REVERT: A  444 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8306 (tm-30)
  outliers start: 61
  outliers final: 37
  residues processed: 256
  average time/residue: 0.1835
  time to fit residues: 69.2768
Evaluate side-chains
  260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 215
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  308 CYS
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain C residue  482 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  457 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0040
   chunk 120 optimal weight:    0.9990
   chunk 126 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 119 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 11 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN
B 403 GLN
B 452 HIS
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.079100 restraints weight = 28731.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.081391 restraints weight = 15227.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.082858 restraints weight = 9906.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10143  Z= 0.176
  Angle     :  0.738  12.339  13821  Z= 0.334
  Chirality :  0.042   0.331   1730
  Planarity :  0.004   0.034   1725
  Dihedral  :  4.254  52.068   1479
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 27.68 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.24), residues: 1332
  helix:  0.57 (0.18), residues: 915
  sheet: -1.12 (1.01), residues: 30
  loop : -1.72 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 461 
 HIS   0.005   0.001   HIS C 452 
 PHE   0.010   0.001   PHE A 134 
 TYR   0.008   0.001   TYR C 325 
 ARG   0.003   0.000   ARG B 246 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 217
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 MET cc_start: 0.8802 (ppp) cc_final: 0.8526 (ppp)
REVERT: B  127 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8562 (tm)
REVERT: B  141 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9077 (mm)
REVERT: B  179 GLU cc_start: 0.8541 (tp30) cc_final: 0.8327 (tp30)
REVERT: B  225 GLU cc_start: 0.8814 (mp0) cc_final: 0.8454 (mp0)
REVERT: B  282 MET cc_start: 0.8420 (ttt) cc_final: 0.8192 (ttp)
REVERT: B  302 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8707 (pp)
REVERT: B  363 CYS cc_start: 0.8652 (m) cc_final: 0.8088 (t)
REVERT: B  387 MET cc_start: 0.8096 (mmp) cc_final: 0.7858 (mmp)
REVERT: B  413 LYS cc_start: 0.9131 (mttp) cc_final: 0.8869 (mttm)
REVERT: B  431 ILE cc_start: 0.8619 (mt) cc_final: 0.8406 (tt)
REVERT: B  465 ARG cc_start: 0.7711 (mtt90) cc_final: 0.7510 (mtp85)
REVERT: C  186 ASP cc_start: 0.8611 (t70) cc_final: 0.7976 (t0)
REVERT: C  313 HIS cc_start: 0.8974 (m90) cc_final: 0.8078 (m-70)
REVERT: C  328 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8115 (t80)
REVERT: C  334 TYR cc_start: 0.8045 (m-10) cc_final: 0.7656 (t80)
REVERT: C  408 SER cc_start: 0.6947 (m) cc_final: 0.6638 (t)
REVERT: C  418 LEU cc_start: 0.9257 (tt) cc_final: 0.9024 (pp)
REVERT: A   50 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7376 (tpt90)
REVERT: A   94 GLU cc_start: 0.8443 (tp30) cc_final: 0.8186 (tp30)
REVERT: A  229 MET cc_start: 0.8362 (tmm) cc_final: 0.8153 (tmm)
REVERT: A  267 MET cc_start: 0.8793 (tpt) cc_final: 0.8379 (mmm)
REVERT: A  292 MET cc_start: 0.7874 (mpp) cc_final: 0.7519 (mmm)
REVERT: A  302 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: A  307 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8710 (tp)
REVERT: A  332 ASN cc_start: 0.8439 (t0) cc_final: 0.7739 (m-40)
REVERT: A  359 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8872 (tt)
REVERT: A  363 CYS cc_start: 0.9135 (m) cc_final: 0.8275 (m)
REVERT: A  403 GLN cc_start: 0.9104 (tp40) cc_final: 0.8616 (tp40)
REVERT: A  418 LEU cc_start: 0.9202 (mt) cc_final: 0.8659 (mt)
  outliers start: 55
  outliers final: 35
  residues processed: 248
  average time/residue: 0.2006
  time to fit residues: 74.1537
Evaluate side-chains
  248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 206
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  308 CYS
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  457 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 104 optimal weight:    7.9990
   chunk 86 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 403 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.078867 restraints weight = 28887.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.081157 restraints weight = 15262.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.082691 restraints weight = 9904.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10143  Z= 0.187
  Angle     :  0.742  11.898  13821  Z= 0.336
  Chirality :  0.043   0.302   1730
  Planarity :  0.004   0.036   1725
  Dihedral  :  4.184  51.956   1479
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 28.16 %
    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: -0.12 (0.24), residues: 1332
  helix:  0.64 (0.18), residues: 915
  sheet: -1.10 (1.02), residues: 30
  loop : -1.63 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 461 
 HIS   0.005   0.001   HIS C 452 
 PHE   0.011   0.001   PHE C 192 
 TYR   0.018   0.001   TYR B 485 
 ARG   0.003   0.000   ARG B 246 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 214
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 MET cc_start: 0.8793 (ppp) cc_final: 0.8502 (ppp)
REVERT: B  127 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8587 (tm)
REVERT: B  141 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9073 (mm)
REVERT: B  179 GLU cc_start: 0.8567 (tp30) cc_final: 0.8338 (tp30)
REVERT: B  225 GLU cc_start: 0.8830 (mp0) cc_final: 0.8461 (mp0)
REVERT: B  282 MET cc_start: 0.8466 (ttt) cc_final: 0.8219 (ttp)
REVERT: B  302 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8730 (pp)
REVERT: B  363 CYS cc_start: 0.8586 (m) cc_final: 0.8095 (t)
REVERT: B  387 MET cc_start: 0.8161 (mmp) cc_final: 0.7454 (mmm)
REVERT: B  431 ILE cc_start: 0.8657 (mt) cc_final: 0.8447 (tt)
REVERT: B  465 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7509 (mtp85)
REVERT: C  186 ASP cc_start: 0.8673 (t70) cc_final: 0.7991 (t0)
REVERT: C  313 HIS cc_start: 0.8961 (m90) cc_final: 0.8060 (m-70)
REVERT: C  328 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: C  334 TYR cc_start: 0.7957 (m-10) cc_final: 0.7602 (t80)
REVERT: C  408 SER cc_start: 0.6794 (m) cc_final: 0.6474 (t)
REVERT: C  418 LEU cc_start: 0.9250 (tt) cc_final: 0.9021 (pp)
REVERT: A   50 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7431 (tpt90)
REVERT: A   94 GLU cc_start: 0.8429 (tp30) cc_final: 0.8172 (tp30)
REVERT: A  267 MET cc_start: 0.8822 (tpt) cc_final: 0.8426 (mmm)
REVERT: A  292 MET cc_start: 0.7849 (mpp) cc_final: 0.7528 (mmm)
REVERT: A  307 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8814 (tp)
REVERT: A  332 ASN cc_start: 0.8338 (t0) cc_final: 0.7720 (m-40)
REVERT: A  359 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8912 (tt)
REVERT: A  363 CYS cc_start: 0.9138 (m) cc_final: 0.8252 (m)
REVERT: A  366 GLU cc_start: 0.8166 (tt0) cc_final: 0.7937 (tt0)
REVERT: A  418 LEU cc_start: 0.9226 (mt) cc_final: 0.8693 (mt)
  outliers start: 54
  outliers final: 38
  residues processed: 246
  average time/residue: 0.1870
  time to fit residues: 67.5310
Evaluate side-chains
  250 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 206
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  308 CYS
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 111 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0770
   chunk 104 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B 403 GLN
C 394 GLN
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.097028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.078915 restraints weight = 28915.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.081148 restraints weight = 15405.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.082719 restraints weight = 10154.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10143  Z= 0.184
  Angle     :  0.769  11.620  13821  Z= 0.344
  Chirality :  0.044   0.353   1730
  Planarity :  0.004   0.035   1725
  Dihedral  :  4.156  52.190   1479
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 29.50 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1332
  helix:  0.75 (0.18), residues: 918
  sheet: -1.06 (1.02), residues: 30
  loop : -1.57 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 461 
 HIS   0.007   0.001   HIS C 452 
 PHE   0.013   0.001   PHE C 192 
 TYR   0.021   0.001   TYR B 305 
 ARG   0.003   0.000   ARG B 246 

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 217
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 MET cc_start: 0.8797 (ppp) cc_final: 0.8503 (ppp)
REVERT: B  127 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8547 (tm)
REVERT: B  141 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9055 (mm)
REVERT: B  179 GLU cc_start: 0.8558 (tp30) cc_final: 0.8352 (tp30)
REVERT: B  225 GLU cc_start: 0.8772 (mp0) cc_final: 0.8288 (mp0)
REVERT: B  282 MET cc_start: 0.8551 (ttt) cc_final: 0.8277 (ppp)
REVERT: B  302 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8707 (pp)
REVERT: B  363 CYS cc_start: 0.8589 (m) cc_final: 0.8091 (t)
REVERT: B  387 MET cc_start: 0.8188 (mmp) cc_final: 0.7754 (mmp)
REVERT: C  186 ASP cc_start: 0.8645 (t70) cc_final: 0.7981 (t0)
REVERT: C  313 HIS cc_start: 0.8949 (m90) cc_final: 0.8048 (m-70)
REVERT: C  328 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8123 (t80)
REVERT: C  334 TYR cc_start: 0.7905 (m-10) cc_final: 0.7574 (t80)
REVERT: C  408 SER cc_start: 0.6725 (m) cc_final: 0.6454 (t)
REVERT: C  418 LEU cc_start: 0.9246 (tt) cc_final: 0.9037 (pp)
REVERT: A   50 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7423 (tpt90)
REVERT: A   94 GLU cc_start: 0.8413 (tp30) cc_final: 0.8159 (tp30)
REVERT: A  102 MET cc_start: 0.8988 (ppp) cc_final: 0.8607 (ppp)
REVERT: A  267 MET cc_start: 0.8833 (tpt) cc_final: 0.8420 (mmm)
REVERT: A  292 MET cc_start: 0.7802 (mpp) cc_final: 0.7499 (mmm)
REVERT: A  302 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8779 (pp)
REVERT: A  307 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8791 (tp)
REVERT: A  332 ASN cc_start: 0.8287 (t0) cc_final: 0.7663 (m-40)
REVERT: A  359 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8839 (tt)
REVERT: A  363 CYS cc_start: 0.9151 (m) cc_final: 0.8254 (m)
REVERT: A  403 GLN cc_start: 0.8910 (tp40) cc_final: 0.8411 (tm-30)
REVERT: A  418 LEU cc_start: 0.9220 (mt) cc_final: 0.8675 (mt)
  outliers start: 45
  outliers final: 33
  residues processed: 243
  average time/residue: 0.1853
  time to fit residues: 66.0830
Evaluate side-chains
  248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 208
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  475 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  308 CYS
Chi-restraints excluded: chain C residue  328 PHE
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  441 ILE
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 75 optimal weight:    0.1980
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 403 GLN
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.096572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.078555 restraints weight = 28674.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.080827 restraints weight = 15325.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.082221 restraints weight = 10037.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.6078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10143  Z= 0.192
  Angle     :  0.776  11.593  13821  Z= 0.350
  Chirality :  0.044   0.332   1730
  Planarity :  0.004   0.035   1725
  Dihedral  :  4.168  52.061   1479
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 29.12 %
    Favored  : 66.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1332
  helix:  0.67 (0.18), residues: 936
  sheet: -1.01 (1.02), residues: 30
  loop : -1.56 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 461 
 HIS   0.007   0.001   HIS C 452 
 PHE   0.013   0.001   PHE C 192 
 TYR   0.024   0.001   TYR B 305 
 ARG   0.003   0.000   ARG B 246 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3062.87 seconds
wall clock time: 55 minutes 48.02 seconds (3348.02 seconds total)