Starting phenix.real_space_refine
on Mon Apr 28 11:42:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j15_61068/04_2025/9j15_61068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j15_61068/04_2025/9j15_61068.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/9j15_61068/04_2025/9j15_61068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j15_61068/04_2025/9j15_61068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j15_61068/04_2025/9j15_61068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j15_61068/04_2025/9j15_61068.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=   0.052
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-5669/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: 6.90, per 1000 atoms: 0.93
  Number of scatterers: 7458
  At special positions: 0
  Unit cell: (111.1, 95.7, 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=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " distance=2.02

  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.90
  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: 3.994A  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: 4.475A  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: 3.894A  pdb=" N   ALA A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 114 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 3.684A  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: 3.522A  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: 3.910A  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: 3.559A  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: 4.055A  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: 3.706A  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: 3.661A  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: 3.961A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
      removed outlier: 4.073A  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: 4.150A  pdb=" N   MET B  14 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
      removed outlier: 3.646A  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: 3.727A  pdb=" N   PHE B  31 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 53
      removed outlier: 3.650A  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: 4.329A  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: 3.770A  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: 3.561A  pdb=" N   GLY B 209 " --> pdb=" O   ILE B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 267
      removed outlier: 3.745A  pdb=" N   ALA B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
      removed outlier: 3.563A  pdb=" N   ILE B 278 " --> pdb=" O   MET B 274 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
      removed outlier: 4.070A  pdb=" N   SER B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 4.772A  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: 4.490A  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: 3.625A  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: 3.635A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLY B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.577A  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: 3.962A  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: 7.308A  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: 1.99

  Time building geometry restraints manager: 2.17 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: 1296
        1.33 -     1.45: 2008
        1.45 -     1.58: 4210
        1.58 -     1.70: 0
        1.70 -     1.83: 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 1.06e+01
  bond pdb=" CA  VAL B 397 "
       pdb=" CB  VAL B 397 "
    ideal  model  delta    sigma   weight residual
    1.540  1.504  0.036 1.15e-02 7.56e+03 9.94e+00
  bond pdb=" C   PHE A 396 "
       pdb=" O   PHE A 396 "
    ideal  model  delta    sigma   weight residual
    1.234  1.200  0.034 1.23e-02 6.61e+03 7.61e+00
  bond pdb=" C   PHE B 396 "
       pdb=" O   PHE B 396 "
    ideal  model  delta    sigma   weight residual
    1.234  1.201  0.034 1.23e-02 6.61e+03 7.52e+00
  bond pdb=" N   PHE B 396 "
       pdb=" CA  PHE B 396 "
    ideal  model  delta    sigma   weight residual
    1.455  1.422  0.033 1.30e-02 5.92e+03 6.38e+00
  ... (remaining 7603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 9648
        1.68 -     3.36: 551
        3.36 -     5.04: 85
        5.04 -     6.71: 42
        6.71 -     8.39: 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  118.82   -7.63 1.35e+00 5.49e-01 3.19e+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  118.78   -7.59 1.35e+00 5.49e-01 3.16e+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  102.22    7.84 1.51e+00 4.39e-01 2.69e+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  102.32    7.74 1.51e+00 4.39e-01 2.63e+01
  angle pdb=" N   PHE B 396 "
        pdb=" CA  PHE B 396 "
        pdb=" C   PHE B 396 "
      ideal   model   delta    sigma   weight residual
     110.20  118.06   -7.86 1.58e+00 4.01e-01 2.47e+01
  ... (remaining 10337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.49: 3804
        9.49 -    18.98: 452
       18.98 -    28.47: 126
       28.47 -    37.96: 36
       37.96 -    47.45: 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 -156.39  -23.61     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 -156.40  -23.60     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 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 4423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1142
       0.091 -    0.182: 96
       0.182 -    0.272: 10
       0.272 -    0.363: 0
       0.363 -    0.454: 2
  Chirality restraints: 1250
  Sorted by residual:
  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 5.16e+00
  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 5.12e+00
  chirality pdb=" CA  ASN B 432 "
            pdb=" N   ASN B 432 "
            pdb=" C   ASN B 432 "
            pdb=" CB  ASN B 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 1.18e+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 1.17e+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 3.85e+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: 2548
        2.85 -     3.37: 6790
        3.37 -     3.88: 11256
        3.88 -     4.39: 13228
        4.39 -     4.90: 23079
  Nonbonded interactions: 56901
  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
     2.369 3.040
  nonbonded pdb=" OE1 GLU A  43 "
            pdb=" OG1 THR A 412 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OG  SER A  73 "
            pdb=" OD1 ASN A  75 "
     model   vdw
     2.435 3.040
  ... (remaining 56896 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.950
  Find NCS groups from input model:        0.130
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
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= 0.312
  Angle     :  0.965   8.393  10354  Z= 0.529
  Chirality :  0.059   0.454   1250
  Planarity :  0.006   0.049   1272
  Dihedral  :  9.605  47.445   2608
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 1.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  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 A 146 
 ARG   0.005   0.001   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.35879 (  294)
  hydrogen bonds       : angle      11.18167 (  846)
  SS BOND              : bond        0.00652 (    6)
  SS BOND              : angle       1.53956 (   12)
  covalent geometry    : bond        0.00681 ( 7608)
  covalent geometry    : angle       0.96440 (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
  232 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7896 (mtm180)
REVERT: A  108 ASP cc_start: 0.8623 (m-30) cc_final: 0.8307 (m-30)
REVERT: A  187 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7550 (mtm180)
REVERT: A  228 THR cc_start: 0.8693 (t) cc_final: 0.8338 (m)
REVERT: A  353 LEU cc_start: 0.8542 (tp) cc_final: 0.8319 (tp)
REVERT: A  354 TYR cc_start: 0.8125 (t80) cc_final: 0.7705 (t80)
REVERT: A  378 ASP cc_start: 0.8031 (t0) cc_final: 0.7711 (t0)
REVERT: A  404 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8119 (mtpp)
REVERT: A  482 ASN cc_start: 0.8347 (m-40) cc_final: 0.7997 (m110)
REVERT: A  496 MET cc_start: 0.6570 (ttp) cc_final: 0.6188 (ttm)
REVERT: B  104 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7814 (mtm-85)
REVERT: B  108 ASP cc_start: 0.8689 (m-30) cc_final: 0.8299 (m-30)
REVERT: B  187 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7660 (mtm180)
REVERT: B  228 THR cc_start: 0.8707 (t) cc_final: 0.8322 (m)
REVERT: B  353 LEU cc_start: 0.8532 (tp) cc_final: 0.8307 (tp)
REVERT: B  354 TYR cc_start: 0.8085 (t80) cc_final: 0.7632 (t80)
REVERT: B  378 ASP cc_start: 0.8078 (t0) cc_final: 0.7740 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2329
  time to fit residues: 69.2247
Evaluate side-chains
  138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0470
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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
B  95 ASN
B 147 ASN
B 160 HIS
B 432 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.147920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.118214 restraints weight = 9043.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.86
r_work: 0.3001 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7614  Z= 0.113
  Angle     :  0.581   5.218  10354  Z= 0.309
  Chirality :  0.041   0.135   1250
  Planarity :  0.005   0.032   1272
  Dihedral  :  5.458  18.826   1062
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.42 %
    Favored  : 85.91 %
  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: -4.65 (0.20), residues: 1004
  helix: -2.96 (0.16), residues: 554
  sheet:  None (None), residues: 0
  loop : -3.17 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 297 
 PHE   0.017   0.001   PHE B 280 
 TYR   0.018   0.002   TYR B 419 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04425 (  294)
  hydrogen bonds       : angle       5.03752 (  846)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.77399 (   12)
  covalent geometry    : bond        0.00248 ( 7608)
  covalent geometry    : angle       0.58064 (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
  164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8936 (m-30) cc_final: 0.8665 (m-30)
REVERT: A  132 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7973 (p90)
REVERT: A  187 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7730 (mtm180)
REVERT: A  228 THR cc_start: 0.8725 (t) cc_final: 0.8411 (m)
REVERT: A  378 ASP cc_start: 0.7955 (t0) cc_final: 0.7572 (t0)
REVERT: A  404 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8369 (mtpp)
REVERT: A  482 ASN cc_start: 0.8644 (m-40) cc_final: 0.8190 (m110)
REVERT: A  496 MET cc_start: 0.6753 (ttp) cc_final: 0.6270 (ttm)
REVERT: B  108 ASP cc_start: 0.8884 (m-30) cc_final: 0.8625 (m-30)
REVERT: B  132 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7978 (p90)
REVERT: B  187 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7765 (mtm180)
REVERT: B  228 THR cc_start: 0.8788 (t) cc_final: 0.8471 (m)
REVERT: B  268 LYS cc_start: 0.7951 (mttm) cc_final: 0.7727 (mtmt)
REVERT: B  311 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8586 (mt)
REVERT: B  378 ASP cc_start: 0.7834 (t0) cc_final: 0.7503 (t0)
REVERT: B  482 ASN cc_start: 0.8682 (m-40) cc_final: 0.8241 (m110)
  outliers start: 21
  outliers final: 6
  residues processed: 156
  average time/residue: 0.1693
  time to fit residues: 36.6458
Evaluate side-chains
  133 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  311 ILE
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:    0.0470
   chunk 59 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 23 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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
A 432 ASN
B 147 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.135655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.105139 restraints weight = 9249.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 1.86
r_work: 0.2971 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3171

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= 0.098
  Angle     :  0.520   5.161  10354  Z= 0.276
  Chirality :  0.040   0.154   1250
  Planarity :  0.004   0.029   1272
  Dihedral  :  4.884  17.067   1062
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 12.82 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.23), residues: 1004
  helix: -1.71 (0.19), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.82 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  11 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.013   0.001   PHE B 280 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  294)
  hydrogen bonds       : angle       4.29229 (  846)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.73160 (   12)
  covalent geometry    : bond        0.00219 ( 7608)
  covalent geometry    : angle       0.52020 (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
  165 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  108 ASP cc_start: 0.8889 (m-30) cc_final: 0.8607 (m-30)
REVERT: A  122 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: A  187 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7602 (mtm180)
REVERT: A  378 ASP cc_start: 0.7863 (t0) cc_final: 0.7550 (t0)
REVERT: A  482 ASN cc_start: 0.8758 (m-40) cc_final: 0.8348 (m110)
REVERT: A  496 MET cc_start: 0.6672 (ttp) cc_final: 0.6159 (ttm)
REVERT: B  102 ILE cc_start: 0.9018 (tt) cc_final: 0.8807 (tt)
REVERT: B  108 ASP cc_start: 0.8876 (m-30) cc_final: 0.8553 (m-30)
REVERT: B  122 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8708 (mp)
REVERT: B  187 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7672 (mtm180)
REVERT: B  378 ASP cc_start: 0.7822 (t0) cc_final: 0.7479 (t0)
REVERT: B  482 ASN cc_start: 0.8753 (m-40) cc_final: 0.8491 (m110)
  outliers start: 26
  outliers final: 9
  residues processed: 154
  average time/residue: 0.1982
  time to fit residues: 41.2533
Evaluate side-chains
  130 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  311 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 70 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 81 optimal weight:    0.4980
   chunk 94 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.133844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.102978 restraints weight = 9308.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.87
r_work: 0.2930 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3487

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= 0.124
  Angle     :  0.540   6.057  10354  Z= 0.282
  Chirality :  0.041   0.148   1250
  Planarity :  0.004   0.032   1272
  Dihedral  :  4.770  18.243   1062
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.97 %
    Favored  : 82.61 %
  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: -2.51 (0.25), residues: 1004
  helix: -0.97 (0.21), residues: 576
  sheet: -3.12 (1.08), residues: 20
  loop : -2.54 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 335 
 HIS   0.002   0.001   HIS A 160 
 PHE   0.012   0.001   PHE B 368 
 TYR   0.010   0.001   TYR B 343 
 ARG   0.003   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  294)
  hydrogen bonds       : angle       4.16370 (  846)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       0.70693 (   12)
  covalent geometry    : bond        0.00292 ( 7608)
  covalent geometry    : angle       0.53976 (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
  149 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.9056 (tt) cc_final: 0.8803 (tt)
REVERT: A  108 ASP cc_start: 0.8892 (m-30) cc_final: 0.8590 (m-30)
REVERT: A  182 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7777 (ttm110)
REVERT: A  187 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7651 (mtm180)
REVERT: A  378 ASP cc_start: 0.7801 (t0) cc_final: 0.7443 (t0)
REVERT: A  496 MET cc_start: 0.6670 (ttp) cc_final: 0.6161 (ttm)
REVERT: B  102 ILE cc_start: 0.9059 (tt) cc_final: 0.8811 (tt)
REVERT: B  108 ASP cc_start: 0.8888 (m-30) cc_final: 0.8550 (m-30)
REVERT: B  187 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7737 (mtm180)
REVERT: B  332 SER cc_start: 0.8800 (m) cc_final: 0.8567 (t)
REVERT: B  378 ASP cc_start: 0.7787 (t0) cc_final: 0.7419 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 139
  average time/residue: 0.1776
  time to fit residues: 33.9080
Evaluate side-chains
  142 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  311 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.0770
   chunk 51 optimal weight:    9.9990
   chunk 80 optimal weight:    0.2980
   chunk 45 optimal weight:    0.0670
   chunk 70 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.3076

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.137400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.106890 restraints weight = 9103.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.82
r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7614  Z= 0.077
  Angle     :  0.483   5.477  10354  Z= 0.252
  Chirality :  0.039   0.146   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.329  15.231   1062
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.48 %
    Favored  : 81.98 %
  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: -1.72 (0.26), residues: 1004
  helix: -0.26 (0.22), residues: 570
  sheet: -3.13 (1.04), residues: 20
  loop : -2.29 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 335 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.011   0.001   PHE B 280 
 TYR   0.017   0.001   TYR A 343 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02403 (  294)
  hydrogen bonds       : angle       3.78280 (  846)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       0.59727 (   12)
  covalent geometry    : bond        0.00166 ( 7608)
  covalent geometry    : angle       0.48262 (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
  172 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.6985 (mtmt) cc_final: 0.6567 (mtmm)
REVERT: A  102 ILE cc_start: 0.9004 (tt) cc_final: 0.8766 (tt)
REVERT: A  108 ASP cc_start: 0.8908 (m-30) cc_final: 0.8620 (m-30)
REVERT: A  182 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7722 (ttm110)
REVERT: A  187 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7589 (mtm180)
REVERT: A  378 ASP cc_start: 0.7866 (t0) cc_final: 0.7617 (t0)
REVERT: A  479 SER cc_start: 0.9146 (t) cc_final: 0.8758 (p)
REVERT: A  482 ASN cc_start: 0.8554 (m-40) cc_final: 0.8100 (m110)
REVERT: A  496 MET cc_start: 0.6648 (ttp) cc_final: 0.6110 (ttm)
REVERT: B   15 LYS cc_start: 0.6948 (mtmt) cc_final: 0.6534 (mtmm)
REVERT: B  102 ILE cc_start: 0.9011 (tt) cc_final: 0.8786 (tt)
REVERT: B  108 ASP cc_start: 0.8883 (m-30) cc_final: 0.8549 (m-30)
REVERT: B  187 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7684 (mtm180)
REVERT: B  332 SER cc_start: 0.8816 (m) cc_final: 0.8536 (t)
REVERT: B  482 ASN cc_start: 0.8622 (m-40) cc_final: 0.8331 (m110)
REVERT: B  496 MET cc_start: 0.6808 (ttp) cc_final: 0.6437 (ttm)
  outliers start: 20
  outliers final: 5
  residues processed: 165
  average time/residue: 0.2183
  time to fit residues: 47.1532
Evaluate side-chains
  140 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  132 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0170
   chunk 63 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0370
   chunk 88 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 76 optimal weight:    0.1980
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.2896

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.167154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.135296 restraints weight = 9117.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.08
r_work: 0.3329 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7614  Z= 0.077
  Angle     :  0.478   6.185  10354  Z= 0.248
  Chirality :  0.039   0.139   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.122  14.508   1062
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.89 %
    Favored  : 80.58 %
  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: -1.44 (0.26), residues: 1004
  helix:  0.11 (0.23), residues: 584
  sheet: -3.21 (1.00), residues: 20
  loop : -2.46 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 335 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.010   0.001   PHE B 280 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.002   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02438 (  294)
  hydrogen bonds       : angle       3.65466 (  846)
  SS BOND              : bond        0.00162 (    6)
  SS BOND              : angle       0.51835 (   12)
  covalent geometry    : bond        0.00166 ( 7608)
  covalent geometry    : angle       0.47774 (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
  148 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7069 (mtmt) cc_final: 0.6617 (mtmm)
REVERT: A   32 LYS cc_start: 0.8269 (mtmp) cc_final: 0.8065 (mtmm)
REVERT: A  102 ILE cc_start: 0.9091 (tt) cc_final: 0.8862 (tt)
REVERT: A  108 ASP cc_start: 0.8815 (m-30) cc_final: 0.8558 (m-30)
REVERT: A  187 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7732 (mtm180)
REVERT: A  378 ASP cc_start: 0.7831 (t0) cc_final: 0.7516 (t0)
REVERT: A  496 MET cc_start: 0.6798 (ttp) cc_final: 0.6338 (ttm)
REVERT: B  102 ILE cc_start: 0.9119 (tt) cc_final: 0.8895 (tt)
REVERT: B  108 ASP cc_start: 0.8847 (m-30) cc_final: 0.8549 (m-30)
REVERT: B  187 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7797 (mtm180)
REVERT: B  222 ASP cc_start: 0.7472 (t0) cc_final: 0.7202 (t0)
REVERT: B  332 SER cc_start: 0.8967 (m) cc_final: 0.8758 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 143
  average time/residue: 0.2119
  time to fit residues: 40.4046
Evaluate side-chains
  137 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  223 LYS
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:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.135772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.105305 restraints weight = 9205.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.77
r_work: 0.2963 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7614  Z= 0.095
  Angle     :  0.494   6.197  10354  Z= 0.256
  Chirality :  0.040   0.144   1250
  Planarity :  0.003   0.033   1272
  Dihedral  :  4.154  14.926   1062
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.77 %
    Favored  : 80.71 %
  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: -0.91 (0.27), residues: 1004
  helix:  0.46 (0.23), residues: 570
  sheet: -3.43 (0.97), residues: 20
  loop : -2.00 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 335 
 HIS   0.001   0.001   HIS A 160 
 PHE   0.010   0.001   PHE A 132 
 TYR   0.009   0.001   TYR B 343 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02886 (  294)
  hydrogen bonds       : angle       3.70554 (  846)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       0.56430 (   12)
  covalent geometry    : bond        0.00220 ( 7608)
  covalent geometry    : angle       0.49368 (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
  144 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8097 (mtmp) cc_final: 0.7858 (mtmm)
REVERT: A  102 ILE cc_start: 0.9038 (tt) cc_final: 0.8796 (tt)
REVERT: A  108 ASP cc_start: 0.8906 (m-30) cc_final: 0.8636 (m-30)
REVERT: A  187 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7575 (mtm180)
REVERT: A  378 ASP cc_start: 0.7807 (t0) cc_final: 0.7519 (t0)
REVERT: A  496 MET cc_start: 0.6670 (ttp) cc_final: 0.6138 (ttm)
REVERT: B  102 ILE cc_start: 0.9031 (tt) cc_final: 0.8796 (tt)
REVERT: B  108 ASP cc_start: 0.8909 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  187 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7595 (mtm180)
REVERT: B  332 SER cc_start: 0.8816 (m) cc_final: 0.8543 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 137
  average time/residue: 0.2128
  time to fit residues: 38.4811
Evaluate side-chains
  136 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  496 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 30 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.134365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.102206 restraints weight = 9356.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.97
r_work: 0.2908 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7614  Z= 0.118
  Angle     :  0.524   6.565  10354  Z= 0.269
  Chirality :  0.041   0.148   1250
  Planarity :  0.003   0.034   1272
  Dihedral  :  4.325  16.504   1062
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.42 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.27), residues: 1004
  helix:  0.56 (0.23), residues: 572
  sheet: -3.45 (1.02), residues: 20
  loop : -1.91 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 335 
 HIS   0.002   0.001   HIS B 160 
 PHE   0.011   0.001   PHE B 368 
 TYR   0.010   0.001   TYR B 375 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  294)
  hydrogen bonds       : angle       3.82221 (  846)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       0.63319 (   12)
  covalent geometry    : bond        0.00284 ( 7608)
  covalent geometry    : angle       0.52424 (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: 10
    poor density    : 131
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.9122 (tt) cc_final: 0.8869 (tt)
REVERT: A  108 ASP cc_start: 0.9010 (m-30) cc_final: 0.8734 (m-30)
REVERT: A  187 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7594 (mtm180)
REVERT: A  378 ASP cc_start: 0.7710 (t0) cc_final: 0.7265 (t0)
REVERT: A  496 MET cc_start: 0.6617 (ttp) cc_final: 0.6367 (ttp)
REVERT: B  102 ILE cc_start: 0.9107 (tt) cc_final: 0.8865 (tt)
REVERT: B  108 ASP cc_start: 0.9026 (m-30) cc_final: 0.8732 (m-30)
REVERT: B  187 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7671 (mtm180)
REVERT: B  332 SER cc_start: 0.8829 (m) cc_final: 0.8581 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 134
  average time/residue: 0.2086
  time to fit residues: 37.1672
Evaluate side-chains
  136 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  496 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.0070
   chunk 9 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.136938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104954 restraints weight = 9215.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.96
r_work: 0.2958 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7614  Z= 0.087
  Angle     :  0.496   6.929  10354  Z= 0.254
  Chirality :  0.040   0.143   1250
  Planarity :  0.003   0.035   1272
  Dihedral  :  4.164  15.328   1062
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 19.92 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.27), residues: 1004
  helix:  0.86 (0.23), residues: 570
  sheet: -3.49 (1.00), residues: 20
  loop : -1.85 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.015   0.001   PHE B 280 
 TYR   0.010   0.001   TYR B 343 
 ARG   0.001   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02689 (  294)
  hydrogen bonds       : angle       3.69637 (  846)
  SS BOND              : bond        0.00188 (    6)
  SS BOND              : angle       0.55015 (   12)
  covalent geometry    : bond        0.00197 ( 7608)
  covalent geometry    : angle       0.49627 (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
  136 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.9064 (tt) cc_final: 0.8811 (tt)
REVERT: A  108 ASP cc_start: 0.8980 (m-30) cc_final: 0.8708 (m-30)
REVERT: A  187 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7792 (mtm180)
REVERT: A  378 ASP cc_start: 0.7876 (t0) cc_final: 0.7504 (t0)
REVERT: A  496 MET cc_start: 0.6631 (ttp) cc_final: 0.6078 (ttm)
REVERT: B  102 ILE cc_start: 0.9071 (tt) cc_final: 0.8828 (tt)
REVERT: B  108 ASP cc_start: 0.8978 (m-30) cc_final: 0.8687 (m-30)
REVERT: B  187 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7651 (mtm180)
REVERT: B  332 SER cc_start: 0.8839 (m) cc_final: 0.8576 (t)
  outliers start: 7
  outliers final: 7
  residues processed: 132
  average time/residue: 0.2081
  time to fit residues: 37.0366
Evaluate side-chains
  137 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  496 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:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.4362

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.131692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.100356 restraints weight = 9384.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.91
r_work: 0.2871 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7614  Z= 0.168
  Angle     :  0.575   7.261  10354  Z= 0.293
  Chirality :  0.043   0.155   1250
  Planarity :  0.004   0.034   1272
  Dihedral  :  4.569  18.688   1062
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 19.80 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.27), residues: 1004
  helix:  0.68 (0.23), residues: 574
  sheet: -3.60 (0.96), residues: 20
  loop : -1.99 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.015   0.002   PHE B 280 
 TYR   0.011   0.001   TYR B 375 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04083 (  294)
  hydrogen bonds       : angle       4.01256 (  846)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       0.76052 (   12)
  covalent geometry    : bond        0.00409 ( 7608)
  covalent geometry    : angle       0.57456 (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
  142 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.9109 (tt) cc_final: 0.8834 (tt)
REVERT: A  108 ASP cc_start: 0.8973 (m-30) cc_final: 0.8725 (m-30)
REVERT: A  187 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7903 (mtm180)
REVERT: A  378 ASP cc_start: 0.7864 (t0) cc_final: 0.7327 (t0)
REVERT: A  496 MET cc_start: 0.6704 (ttp) cc_final: 0.6407 (ttp)
REVERT: B  102 ILE cc_start: 0.9121 (tt) cc_final: 0.8868 (tt)
REVERT: B  108 ASP cc_start: 0.8965 (m-30) cc_final: 0.8674 (m-30)
REVERT: B  187 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7909 (mtm180)
REVERT: B  332 SER cc_start: 0.8890 (m) cc_final: 0.8618 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 137
  average time/residue: 0.2100
  time to fit residues: 38.1098
Evaluate side-chains
  133 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  496 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 73 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 83 optimal weight:    0.1980
   chunk 57 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.135885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.104593 restraints weight = 9230.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.89
r_work: 0.2952 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7614  Z= 0.089
  Angle     :  0.514   6.593  10354  Z= 0.262
  Chirality :  0.040   0.146   1250
  Planarity :  0.003   0.035   1272
  Dihedral  :  4.290  16.818   1062
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 19.92 %
    Favored  : 79.31 %
  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: -0.39 (0.27), residues: 1004
  helix:  0.98 (0.23), residues: 574
  sheet: -3.51 (1.00), residues: 20
  loop : -1.94 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 335 
 HIS   0.001   0.000   HIS A 160 
 PHE   0.014   0.001   PHE B 280 
 TYR   0.010   0.001   TYR B 375 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02750 (  294)
  hydrogen bonds       : angle       3.76094 (  846)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       1.01934 (   12)
  covalent geometry    : bond        0.00200 ( 7608)
  covalent geometry    : angle       0.51313 (10342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3915.27 seconds
wall clock time: 67 minutes 39.46 seconds (4059.46 seconds total)