Starting phenix.real_space_refine
on Sun May 11 04:13:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j16_61069/05_2025/9j16_61069.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.050
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      56      5.16       5
     C    4836      2.51       5
     N    1202      2.21       5
     O    1364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7458
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3718
          Classifications: {'peptide': 504}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 16, 'TRANS': 487}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'DNA': 1}
          Modifications used: {'5*END': 1}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.33, per 1000 atoms: 0.85
  Number of scatterers: 7458
  At special positions: 0
  Unit cell: (89.1, 118.8, 88, 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      56     16.00
     O    1364      8.00
     N    1202      7.00
     C    4836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.82
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      59.9% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 24
      removed outlier: 4.150A  pdb=" N   MET A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A  15 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A  19 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASP A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A  23 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 3.727A  pdb=" N   PHE A  31 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 53
      removed outlier: 3.650A  pdb=" N   THR A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 4.330A  pdb=" N   CYS A  90 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL A  91 " --> pdb=" O   GLY A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 91'
    Processing helix  chain 'A' and resid 97 through 103
    Processing helix  chain 'A' and resid 106 through 129
      removed outlier: 4.215A  pdb=" N   VAL A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER A 114 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
      removed outlier: 3.662A  pdb=" N   ILE A 144 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 175
      removed outlier: 3.523A  pdb=" N   ALA A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU A 167 " --> pdb=" O   MET A 163 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 175 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
      removed outlier: 3.909A  pdb=" N   ARG A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
      removed outlier: 4.176A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 267
      removed outlier: 3.746A  pdb=" N   ALA A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 3.563A  pdb=" N   ILE A 278 " --> pdb=" O   MET A 274 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 309
      removed outlier: 4.070A  pdb=" N   SER A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.656A  pdb=" N   TRP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 346 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 3.705A  pdb=" N   ILE A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 387
      removed outlier: 4.491A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
      removed outlier: 3.531A  pdb=" N   GLY A 402 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 422
      removed outlier: 3.519A  pdb=" N   ILE A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A 420 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 438 through 451
      removed outlier: 3.636A  pdb=" N   VAL A 445 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLY A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.662A  pdb=" N   ILE A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 477
      removed outlier: 3.684A  pdb=" N   ALA A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 480 through 494
      removed outlier: 3.962A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ILE A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 507
    Processing helix  chain 'B' and resid 6 through 24
      removed outlier: 4.149A  pdb=" N   MET B  14 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B  15 " --> pdb=" O   TRP B  11 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASP B  20 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 31
      removed outlier: 3.726A  pdb=" N   PHE B  31 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 53
      removed outlier: 3.651A  pdb=" N   THR B  53 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 4.330A  pdb=" N   CYS B  90 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 86 through 91'
    Processing helix  chain 'B' and resid 97 through 103
    Processing helix  chain 'B' and resid 106 through 129
      removed outlier: 4.215A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER B 114 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY B 125 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 127 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
      removed outlier: 3.661A  pdb=" N   ILE B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 175
      removed outlier: 3.522A  pdb=" N   ALA B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B 167 " --> pdb=" O   MET B 163 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B 175 " --> pdb=" O   CYS B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.909A  pdb=" N   ARG B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 209
      removed outlier: 4.176A  pdb=" N   ALA B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY B 209 " --> pdb=" O   ILE B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 267
      removed outlier: 3.746A  pdb=" N   ALA B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
      removed outlier: 3.562A  pdb=" N   ILE B 278 " --> pdb=" O   MET B 274 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
      removed outlier: 4.071A  pdb=" N   SER B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ASN B 304 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR B 307 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 352
      removed outlier: 4.656A  pdb=" N   TRP B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 346 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLY B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 3.705A  pdb=" N   ILE B 359 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 387
      removed outlier: 4.491A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   VAL B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA B 387 " --> pdb=" O   VAL B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 402
      removed outlier: 3.531A  pdb=" N   GLY B 402 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 422
      removed outlier: 3.520A  pdb=" N   ILE B 415 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE B 420 " --> pdb=" O   VAL B 416 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 438 through 451
      removed outlier: 3.636A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLY B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B 451 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.662A  pdb=" N   ILE B 456 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 477
      removed outlier: 3.684A  pdb=" N   ALA B 467 " --> pdb=" O   GLU B 463 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
      Proline residue:  B 475  - end of helix
    Processing helix  chain 'B' and resid 480 through 494
      removed outlier: 3.961A  pdb=" N   ALA B 486 " --> pdb=" O   ASN B 482 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ILE B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 507
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136
      removed outlier: 4.070A  pdb=" N   ALA A 135 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235
      removed outlier: 7.307A  pdb=" N   GLU A 234 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 136
      removed outlier: 4.071A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220
    Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 235
      removed outlier: 7.307A  pdb=" N   GLU B 234 " --> pdb=" O   LEU B 243 " (cutoff:3.500A)

    294 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1297
        1.33 -     1.45: 2004
        1.45 -     1.58: 4213
        1.58 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 7608
  Sorted by residual:
  bond pdb=" CA  VAL A 397 "
       pdb=" CB  VAL A 397 "
    ideal  model  delta    sigma   weight residual
    1.540  1.503  0.037 1.15e-02 7.56e+03 1.03e+01
  bond pdb=" CA  VAL B 397 "
       pdb=" CB  VAL B 397 "
    ideal  model  delta    sigma   weight residual
    1.540  1.504  0.037 1.15e-02 7.56e+03 1.01e+01
  bond pdb=" C   PHE A 396 "
       pdb=" O   PHE A 396 "
    ideal  model  delta    sigma   weight residual
    1.234  1.201  0.034 1.23e-02 6.61e+03 7.58e+00
  bond pdb=" C   PHE B 396 "
       pdb=" O   PHE B 396 "
    ideal  model  delta    sigma   weight residual
    1.234  1.201  0.033 1.23e-02 6.61e+03 7.32e+00
  bond pdb=" N   PHE A 396 "
       pdb=" CA  PHE A 396 "
    ideal  model  delta    sigma   weight residual
    1.455  1.423  0.033 1.30e-02 5.92e+03 6.34e+00
  ... (remaining 7603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 9642
        1.68 -     3.35: 557
        3.35 -     5.03: 85
        5.03 -     6.70: 42
        6.70 -     8.38: 16
  Bond angle restraints: 10342
  Sorted by residual:
  angle pdb=" N   VAL A 227 "
        pdb=" CA  VAL A 227 "
        pdb=" CB  VAL A 227 "
      ideal   model   delta    sigma   weight residual
     111.19  118.80   -7.61 1.35e+00 5.49e-01 3.17e+01
  angle pdb=" N   VAL B 227 "
        pdb=" CA  VAL B 227 "
        pdb=" CB  VAL B 227 "
      ideal   model   delta    sigma   weight residual
     111.19  118.79   -7.60 1.35e+00 5.49e-01 3.17e+01
  angle pdb=" N   PHE A 396 "
        pdb=" CA  PHE A 396 "
        pdb=" CB  PHE A 396 "
      ideal   model   delta    sigma   weight residual
     110.06  102.25    7.81 1.51e+00 4.39e-01 2.68e+01
  angle pdb=" N   PHE B 396 "
        pdb=" CA  PHE B 396 "
        pdb=" CB  PHE B 396 "
      ideal   model   delta    sigma   weight residual
     110.06  102.28    7.78 1.51e+00 4.39e-01 2.65e+01
  angle pdb=" N   PHE A 396 "
        pdb=" CA  PHE A 396 "
        pdb=" C   PHE A 396 "
      ideal   model   delta    sigma   weight residual
     110.20  118.06   -7.86 1.58e+00 4.01e-01 2.48e+01
  ... (remaining 10337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.49: 3804
        9.49 -    18.98: 452
       18.98 -    28.46: 126
       28.46 -    37.95: 36
       37.95 -    47.44: 8
  Dihedral angle restraints: 4426
    sinusoidal: 1588
      harmonic: 2838
  Sorted by residual:
  dihedral pdb=" CA  ARG A  36 "
           pdb=" C   ARG A  36 "
           pdb=" N   LYS A  37 "
           pdb=" CA  LYS A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.40  -23.60     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ARG B  36 "
           pdb=" C   ARG B  36 "
           pdb=" N   LYS B  37 "
           pdb=" CA  LYS B  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.41  -23.59     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  PHE B 362 "
           pdb=" C   PHE B 362 "
           pdb=" N   VAL B 363 "
           pdb=" CA  VAL B 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.01  -22.99     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 4423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1145
       0.091 -    0.182: 93
       0.182 -    0.273: 10
       0.273 -    0.363: 0
       0.363 -    0.454: 2
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CB  ILE B  57 "
            pdb=" CA  ILE B  57 "
            pdb=" CG1 ILE B  57 "
            pdb=" CG2 ILE B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.19    0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" CB  ILE A  57 "
            pdb=" CA  ILE A  57 "
            pdb=" CG1 ILE A  57 "
            pdb=" CG2 ILE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.19    0.45 2.00e-01 2.50e+01 5.13e+00
  chirality pdb=" CA  ASN A 432 "
            pdb=" N   ASN A 432 "
            pdb=" C   ASN A 432 "
            pdb=" CB  ASN A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1247 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 430 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.17e+01
        pdb=" C   VAL B 430 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   VAL B 430 "    0.022 2.00e-02 2.50e+03
        pdb=" N   THR B 431 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 430 "   -0.017 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   VAL A 430 "    0.059 2.00e-02 2.50e+03
        pdb=" O   VAL A 430 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR A 431 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 135 "    0.033 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO A 136 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 136 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 136 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2546
        2.85 -     3.37: 6791
        3.37 -     3.88: 11254
        3.88 -     4.39: 13224
        4.39 -     4.90: 23088
  Nonbonded interactions: 56903
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 192 "
            pdb=" OE1 GLU B 463 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OG1 THR A 192 "
            pdb=" OE1 GLU A 463 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OE1 GLU B  43 "
            pdb=" OG1 THR B 412 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OE1 GLU A  43 "
            pdb=" OG1 THR A 412 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OG  SER B  73 "
            pdb=" OD1 ASN B  75 "
     model   vdw
     2.435 3.040
  ... (remaining 56898 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.930
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
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      :  0.007   0.070   7614  Z= 0.311
  Angle     :  0.965   8.377  10354  Z= 0.528
  Chirality :  0.059   0.454   1250
  Planarity :  0.006   0.049   1272
  Dihedral  :  9.605  47.438   2608
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  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: -6.55 (0.15), residues: 1004
  helix: -4.72 (0.07), residues: 558
  sheet:  None (None), residues: 0
  loop : -3.72 (0.22), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 253 
 HIS   0.003   0.001   HIS B 315 
 PHE   0.022   0.002   PHE A 207 
 TYR   0.018   0.002   TYR B 146 
 ARG   0.005   0.001   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.35878 (  294)
  hydrogen bonds       : angle      11.18073 (  846)
  SS BOND              : bond        0.00648 (    6)
  SS BOND              : angle       1.53442 (   12)
  covalent geometry    : bond        0.00680 ( 7608)
  covalent geometry    : angle       0.96456 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8137 (mptt) cc_final: 0.7824 (mtpt)
REVERT: A   26 PHE cc_start: 0.7466 (t80) cc_final: 0.7069 (p90)
REVERT: A  213 ASN cc_start: 0.7785 (m-40) cc_final: 0.7292 (p0)
REVERT: A  378 ASP cc_start: 0.8454 (t0) cc_final: 0.8248 (t0)
REVERT: A  479 SER cc_start: 0.9583 (t) cc_final: 0.8831 (p)
REVERT: B   15 LYS cc_start: 0.7973 (mptt) cc_final: 0.7663 (ttpt)
REVERT: B   26 PHE cc_start: 0.7450 (t80) cc_final: 0.6964 (p90)
REVERT: B  203 MET cc_start: 0.9104 (mtp) cc_final: 0.8820 (mtm)
REVERT: B  213 ASN cc_start: 0.7832 (m-40) cc_final: 0.7455 (p0)
REVERT: B  324 ILE cc_start: 0.8526 (mm) cc_final: 0.8278 (mt)
REVERT: B  479 SER cc_start: 0.9605 (t) cc_final: 0.8831 (p)
REVERT: B  482 ASN cc_start: 0.8265 (m-40) cc_final: 0.8036 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1944
  time to fit residues: 52.5722
Evaluate side-chains
  117 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0770
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 147 ASN
A 160 HIS
A 482 ASN
B  95 ASN
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 160 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.151769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.121500 restraints weight = 9898.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.28
r_work: 0.3177 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7614  Z= 0.110
  Angle     :  0.583   6.373  10354  Z= 0.309
  Chirality :  0.041   0.177   1250
  Planarity :  0.005   0.032   1272
  Dihedral  :  5.426  19.404   1062
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.14 %
    Favored  : 88.83 %
  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: -4.78 (0.20), residues: 1004
  helix: -3.04 (0.15), residues: 572
  sheet:  None (None), residues: 0
  loop : -3.25 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 253 
 HIS   0.003   0.001   HIS B  17 
 PHE   0.013   0.001   PHE B 132 
 TYR   0.015   0.001   TYR B 419 
 ARG   0.003   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  294)
  hydrogen bonds       : angle       4.97735 (  846)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       0.80743 (   12)
  covalent geometry    : bond        0.00244 ( 7608)
  covalent geometry    : angle       0.58287 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8219 (mptt) cc_final: 0.7869 (ttpt)
REVERT: A  102 ILE cc_start: 0.8969 (tt) cc_final: 0.8704 (tt)
REVERT: A  213 ASN cc_start: 0.8041 (m-40) cc_final: 0.7417 (p0)
REVERT: A  247 MET cc_start: 0.9206 (mmm) cc_final: 0.8950 (tpp)
REVERT: A  274 MET cc_start: 0.9010 (mtp) cc_final: 0.8764 (mtm)
REVERT: A  314 PHE cc_start: 0.8606 (t80) cc_final: 0.8386 (t80)
REVERT: A  479 SER cc_start: 0.9318 (t) cc_final: 0.8894 (p)
REVERT: B  102 ILE cc_start: 0.8924 (tt) cc_final: 0.8648 (tt)
REVERT: B  212 MET cc_start: 0.7694 (pmm) cc_final: 0.7139 (mtt)
REVERT: B  213 ASN cc_start: 0.8092 (m-40) cc_final: 0.7468 (p0)
REVERT: B  479 SER cc_start: 0.9354 (t) cc_final: 0.8884 (p)
REVERT: B  482 ASN cc_start: 0.8621 (m-40) cc_final: 0.8339 (m110)
  outliers start: 16
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1531
  time to fit residues: 30.9239
Evaluate side-chains
  107 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 432 ASN
B 147 ASN
B 432 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.116976 restraints weight = 9948.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.29
r_work: 0.3070 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7614  Z= 0.134
  Angle     :  0.563   5.323  10354  Z= 0.300
  Chirality :  0.041   0.163   1250
  Planarity :  0.004   0.031   1272
  Dihedral  :  5.044  18.349   1062
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.91 %
    Favored  : 86.17 %
  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: -3.55 (0.23), residues: 1004
  helix: -1.85 (0.19), residues: 580
  sheet:  None (None), residues: 0
  loop : -3.03 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A  17 
 PHE   0.014   0.001   PHE B 132 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.003   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  294)
  hydrogen bonds       : angle       4.35988 (  846)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.83435 (   12)
  covalent geometry    : bond        0.00316 ( 7608)
  covalent geometry    : angle       0.56261 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8019 (mptt) cc_final: 0.7639 (ttpt)
REVERT: A  102 ILE cc_start: 0.9005 (tt) cc_final: 0.8698 (tt)
REVERT: A  163 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8464 (mmp)
REVERT: A  213 ASN cc_start: 0.8077 (m-40) cc_final: 0.7339 (p0)
REVERT: A  274 MET cc_start: 0.9045 (mtp) cc_final: 0.8793 (mtm)
REVERT: A  479 SER cc_start: 0.9380 (t) cc_final: 0.9166 (p)
REVERT: B  102 ILE cc_start: 0.9006 (tt) cc_final: 0.8699 (tt)
REVERT: B  163 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8459 (mmp)
REVERT: B  213 ASN cc_start: 0.8115 (m-40) cc_final: 0.7413 (p0)
REVERT: B  324 ILE cc_start: 0.8404 (mm) cc_final: 0.8150 (mt)
REVERT: B  479 SER cc_start: 0.9462 (t) cc_final: 0.9015 (p)
REVERT: B  482 ASN cc_start: 0.8725 (m-40) cc_final: 0.8363 (m110)
  outliers start: 23
  outliers final: 12
  residues processed: 119
  average time/residue: 0.1280
  time to fit residues: 23.2796
Evaluate side-chains
  114 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  163 MET
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.0010
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.3586

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.153806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.122728 restraints weight = 9972.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.31
r_work: 0.3236 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7614  Z= 0.081
  Angle     :  0.489   5.236  10354  Z= 0.260
  Chirality :  0.039   0.141   1250
  Planarity :  0.003   0.031   1272
  Dihedral  :  4.486  15.658   1062
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.82 %
    Favored  : 85.28 %
  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: -2.54 (0.25), residues: 1004
  helix: -0.96 (0.21), residues: 574
  sheet:  None (None), residues: 0
  loop : -2.69 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A  17 
 PHE   0.011   0.001   PHE A 368 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.002   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02569 (  294)
  hydrogen bonds       : angle       3.94250 (  846)
  SS BOND              : bond        0.00223 (    6)
  SS BOND              : angle       0.61722 (   12)
  covalent geometry    : bond        0.00176 ( 7608)
  covalent geometry    : angle       0.48875 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8030 (mptt) cc_final: 0.7749 (ttpt)
REVERT: A  102 ILE cc_start: 0.8982 (tt) cc_final: 0.8697 (tt)
REVERT: A  212 MET cc_start: 0.7761 (pmm) cc_final: 0.7292 (mtt)
REVERT: A  213 ASN cc_start: 0.7942 (m-40) cc_final: 0.7356 (p0)
REVERT: B  102 ILE cc_start: 0.8971 (tt) cc_final: 0.8664 (tt)
REVERT: B  213 ASN cc_start: 0.8120 (m-40) cc_final: 0.7329 (p0)
REVERT: B  274 MET cc_start: 0.8988 (mtp) cc_final: 0.8785 (mtm)
REVERT: B  479 SER cc_start: 0.9382 (t) cc_final: 0.8933 (p)
REVERT: B  482 ASN cc_start: 0.8497 (m-40) cc_final: 0.8268 (m110)
  outliers start: 15
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1347
  time to fit residues: 27.2501
Evaluate side-chains
  118 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.0870
   chunk 51 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0270
   chunk 28 optimal weight:    0.0070
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.3834

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN
B 211 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.153456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.122836 restraints weight = 9844.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.27
r_work: 0.3238 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7614  Z= 0.081
  Angle     :  0.485   5.440  10354  Z= 0.257
  Chirality :  0.040   0.144   1250
  Planarity :  0.003   0.032   1272
  Dihedral  :  4.275  15.899   1062
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.69 %
    Favored  : 85.28 %
  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: -1.85 (0.26), residues: 1004
  helix: -0.35 (0.22), residues: 572
  sheet:  None (None), residues: 0
  loop : -2.44 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS A  17 
 PHE   0.010   0.001   PHE B 368 
 TYR   0.011   0.001   TYR B 343 
 ARG   0.002   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02716 (  294)
  hydrogen bonds       : angle       3.80469 (  846)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.54963 (   12)
  covalent geometry    : bond        0.00179 ( 7608)
  covalent geometry    : angle       0.48450 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7871 (mptt) cc_final: 0.7635 (ttpt)
REVERT: A  102 ILE cc_start: 0.9010 (tt) cc_final: 0.8711 (tt)
REVERT: A  124 MET cc_start: 0.8630 (tpp) cc_final: 0.8393 (tpp)
REVERT: A  163 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8343 (mmp)
REVERT: A  212 MET cc_start: 0.7736 (pmm) cc_final: 0.7284 (mtt)
REVERT: A  213 ASN cc_start: 0.8000 (m-40) cc_final: 0.7367 (p0)
REVERT: A  274 MET cc_start: 0.9013 (mtp) cc_final: 0.8779 (mtm)
REVERT: B  102 ILE cc_start: 0.8994 (tt) cc_final: 0.8696 (tt)
REVERT: B  163 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8374 (mmp)
REVERT: B  213 ASN cc_start: 0.8040 (m-40) cc_final: 0.7320 (p0)
REVERT: B  479 SER cc_start: 0.9413 (t) cc_final: 0.9062 (p)
REVERT: B  482 ASN cc_start: 0.8375 (m-40) cc_final: 0.8124 (m110)
  outliers start: 16
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1390
  time to fit residues: 25.8937
Evaluate side-chains
  122 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  163 MET
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.112909 restraints weight = 9952.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.33
r_work: 0.3118 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7614  Z= 0.111
  Angle     :  0.504   5.810  10354  Z= 0.266
  Chirality :  0.042   0.180   1250
  Planarity :  0.003   0.032   1272
  Dihedral  :  4.334  17.127   1062
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 13.20 %
    Favored  : 84.01 %
  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: -1.37 (0.26), residues: 1004
  helix: -0.01 (0.22), residues: 570
  sheet: -3.32 (1.04), residues: 20
  loop : -2.04 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.012   0.001   PHE B 132 
 TYR   0.010   0.001   TYR A 343 
 ARG   0.004   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  294)
  hydrogen bonds       : angle       3.84346 (  846)
  SS BOND              : bond        0.00267 (    6)
  SS BOND              : angle       0.63252 (   12)
  covalent geometry    : bond        0.00265 ( 7608)
  covalent geometry    : angle       0.50416 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7928 (mptt) cc_final: 0.7653 (ttpt)
REVERT: A  102 ILE cc_start: 0.9075 (tt) cc_final: 0.8833 (tt)
REVERT: A  163 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8383 (mmp)
REVERT: A  213 ASN cc_start: 0.8049 (m-40) cc_final: 0.7299 (p0)
REVERT: B  102 ILE cc_start: 0.9061 (tt) cc_final: 0.8818 (tt)
REVERT: B  163 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8357 (mmp)
REVERT: B  213 ASN cc_start: 0.8043 (m-40) cc_final: 0.7273 (p0)
REVERT: B  479 SER cc_start: 0.9480 (t) cc_final: 0.9183 (p)
REVERT: B  482 ASN cc_start: 0.8590 (m-40) cc_final: 0.8250 (m110)
  outliers start: 22
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1488
  time to fit residues: 27.3300
Evaluate side-chains
  122 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  163 MET
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 94 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
** B 141 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 = 0.3581 r_free = 0.3581 target = 0.139309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107879 restraints weight = 9961.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.31
r_work: 0.3051 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7614  Z= 0.194
  Angle     :  0.604   5.663  10354  Z= 0.317
  Chirality :  0.044   0.153   1250
  Planarity :  0.003   0.033   1272
  Dihedral  :  4.768  19.259   1062
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.58 %
    Favored  : 82.99 %
  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: -1.50 (0.26), residues: 1004
  helix: -0.14 (0.22), residues: 578
  sheet: -3.31 (1.05), residues: 20
  loop : -2.11 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 335 
 HIS   0.002   0.001   HIS A 297 
 PHE   0.016   0.002   PHE B 132 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.003   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  294)
  hydrogen bonds       : angle       4.12044 (  846)
  SS BOND              : bond        0.00360 (    6)
  SS BOND              : angle       0.82504 (   12)
  covalent geometry    : bond        0.00478 ( 7608)
  covalent geometry    : angle       0.60417 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7871 (mptt) cc_final: 0.7607 (ttpt)
REVERT: A  102 ILE cc_start: 0.9080 (tt) cc_final: 0.8843 (tt)
REVERT: A  163 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8374 (mmp)
REVERT: A  213 ASN cc_start: 0.8277 (m-40) cc_final: 0.7563 (p0)
REVERT: A  324 ILE cc_start: 0.8601 (mm) cc_final: 0.8342 (mt)
REVERT: B  102 ILE cc_start: 0.9079 (tt) cc_final: 0.8842 (tt)
REVERT: B  163 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8410 (mmp)
REVERT: B  213 ASN cc_start: 0.8255 (m-40) cc_final: 0.7555 (p0)
REVERT: B  243 LEU cc_start: 0.6837 (mt) cc_final: 0.6621 (mt)
REVERT: B  479 SER cc_start: 0.9500 (t) cc_final: 0.9138 (p)
REVERT: B  482 ASN cc_start: 0.8805 (m-40) cc_final: 0.8370 (m110)
  outliers start: 27
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1450
  time to fit residues: 27.4077
Evaluate side-chains
  128 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  163 MET
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  352 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0870
   chunk 30 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.144728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.112802 restraints weight = 9993.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.35
r_work: 0.3118 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7614  Z= 0.092
  Angle     :  0.511   6.325  10354  Z= 0.270
  Chirality :  0.041   0.143   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.414  16.696   1062
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.85 %
    Favored  : 82.36 %
  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: -1.02 (0.27), residues: 1004
  helix:  0.33 (0.23), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.10 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A  17 
 PHE   0.015   0.001   PHE A 314 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.004   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02913 (  294)
  hydrogen bonds       : angle       3.79982 (  846)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.59805 (   12)
  covalent geometry    : bond        0.00210 ( 7608)
  covalent geometry    : angle       0.51134 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7769 (mptt) cc_final: 0.7545 (ttpt)
REVERT: A  102 ILE cc_start: 0.9044 (tt) cc_final: 0.8816 (tt)
REVERT: A  213 ASN cc_start: 0.8150 (m-40) cc_final: 0.7324 (p0)
REVERT: A  324 ILE cc_start: 0.8388 (mm) cc_final: 0.8114 (mt)
REVERT: B  102 ILE cc_start: 0.9052 (tt) cc_final: 0.8825 (tt)
REVERT: B  213 ASN cc_start: 0.8146 (m-40) cc_final: 0.7318 (p0)
REVERT: B  356 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7466 (mpp)
REVERT: B  479 SER cc_start: 0.9468 (t) cc_final: 0.9197 (p)
REVERT: B  482 ASN cc_start: 0.8722 (m-40) cc_final: 0.8351 (m110)
  outliers start: 22
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1571
  time to fit residues: 29.7925
Evaluate side-chains
  130 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 9 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0470
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.5878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.145226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.113312 restraints weight = 9911.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.34
r_work: 0.3123 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7614  Z= 0.096
  Angle     :  0.505   6.584  10354  Z= 0.266
  Chirality :  0.041   0.140   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.254  16.463   1062
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.72 %
    Favored  : 82.49 %
  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: -0.69 (0.27), residues: 1004
  helix:  0.60 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.95 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.011   0.001   PHE A 314 
 TYR   0.009   0.001   TYR B 343 
 ARG   0.004   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03013 (  294)
  hydrogen bonds       : angle       3.71035 (  846)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.57421 (   12)
  covalent geometry    : bond        0.00224 ( 7608)
  covalent geometry    : angle       0.50522 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  102 ILE cc_start: 0.9050 (tt) cc_final: 0.8818 (tt)
REVERT: A  124 MET cc_start: 0.8744 (tpp) cc_final: 0.8521 (tpp)
REVERT: A  213 ASN cc_start: 0.8040 (m-40) cc_final: 0.7284 (p0)
REVERT: A  324 ILE cc_start: 0.8378 (mm) cc_final: 0.8121 (mt)
REVERT: B  102 ILE cc_start: 0.9052 (tt) cc_final: 0.8828 (tt)
REVERT: B  213 ASN cc_start: 0.8153 (m-40) cc_final: 0.7348 (p0)
REVERT: B  356 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7452 (mpp)
REVERT: B  479 SER cc_start: 0.9462 (t) cc_final: 0.9210 (p)
REVERT: B  482 ASN cc_start: 0.8661 (m-40) cc_final: 0.8305 (m110)
  outliers start: 22
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1380
  time to fit residues: 26.2135
Evaluate side-chains
  130 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.144760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.112556 restraints weight = 9974.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.37
r_work: 0.3112 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7614  Z= 0.107
  Angle     :  0.519   6.780  10354  Z= 0.271
  Chirality :  0.041   0.143   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.291  16.355   1062
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.23 %
    Favored  : 82.36 %
  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: -0.54 (0.27), residues: 1004
  helix:  0.76 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.93 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.012   0.001   PHE B 132 
 TYR   0.009   0.001   TYR B 343 
 ARG   0.004   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (  294)
  hydrogen bonds       : angle       3.73585 (  846)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       0.60162 (   12)
  covalent geometry    : bond        0.00256 ( 7608)
  covalent geometry    : angle       0.51899 (10342)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  102 ILE cc_start: 0.9052 (tt) cc_final: 0.8824 (tt)
REVERT: A  124 MET cc_start: 0.8797 (tpp) cc_final: 0.8569 (tpp)
REVERT: A  213 ASN cc_start: 0.8156 (m-40) cc_final: 0.7313 (p0)
REVERT: B  102 ILE cc_start: 0.9071 (tt) cc_final: 0.8843 (tt)
REVERT: B  213 ASN cc_start: 0.8244 (m-40) cc_final: 0.7454 (p0)
REVERT: B  356 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7397 (mpp)
REVERT: B  479 SER cc_start: 0.9450 (t) cc_final: 0.9212 (p)
REVERT: B  482 ASN cc_start: 0.8661 (m-40) cc_final: 0.8303 (m110)
  outliers start: 19
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1410
  time to fit residues: 25.3846
Evaluate side-chains
  131 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0870
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:    0.2980
   chunk 67 optimal weight:    0.0050
   chunk 26 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0170
   chunk 93 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.2410

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.150092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.117927 restraints weight = 9846.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.35
r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7614  Z= 0.081
  Angle     :  0.489   6.942  10354  Z= 0.254
  Chirality :  0.040   0.137   1250
  Planarity :  0.003   0.036   1272
  Dihedral  :  4.022  14.717   1062
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.12 %
    Favored  : 82.11 %
  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: -0.25 (0.28), residues: 1004
  helix:  1.06 (0.23), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.91 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 335 
 HIS   0.000   0.000   HIS A  17 
 PHE   0.011   0.001   PHE A 314 
 TYR   0.010   0.001   TYR B 343 
 ARG   0.004   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02327 (  294)
  hydrogen bonds       : angle       3.53117 (  846)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       0.53284 (   12)
  covalent geometry    : bond        0.00180 ( 7608)
  covalent geometry    : angle       0.48906 (10342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3610.05 seconds
wall clock time: 63 minutes 11.41 seconds (3791.41 seconds total)