Starting phenix.real_space_refine
on Mon Jun 16 08:15:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sz0_25558/06_2025/7sz0_25558.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 10184 atoms to isotropic.
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     134      5.16       5
     C    6316      2.51       5
     N    1810      2.21       5
     O    1956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10216
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4723
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 614, 4723
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 30, 'TRANS': 583}
    Chain: "C"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 385
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "B"
      Number of atoms: 4723
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 614, 4723
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 30, 'TRANS': 583}
    Chain: "D"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 385
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
  Time building chain proxies: 6.89, per 1000 atoms: 0.67
  Number of scatterers: 10216
  At special positions: 0
  Unit cell: (82.0344, 144.64, 129.528, 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     134     16.00
     O    1956      8.00
     N    1810      7.00
     C    6316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=56, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 170 " - pdb=" SG  CYS A 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 271 " - pdb=" SG  CYS A 283 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 305 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 482 " - pdb=" SG  CYS A 491 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 486 " - pdb=" SG  CYS A 499 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 502 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 555 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A 567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 571 " - pdb=" SG  CYS A 593 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 612 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  20 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS C  31 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  42 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 166 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 191 " - pdb=" SG  CYS B 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 195 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 227 " - pdb=" SG  CYS B 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 283 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 287 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 305 " - pdb=" SG  CYS B 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 475 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 482 " - pdb=" SG  CYS B 491 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 499 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 502 " - pdb=" SG  CYS B 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 534 " - pdb=" SG  CYS B 547 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 555 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 558 " - pdb=" SG  CYS B 567 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 571 " - pdb=" SG  CYS B 593 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 604 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 600 " - pdb=" SG  CYS B 612 " distance=2.07
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  20 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  14 " - pdb=" SG  CYS D  31 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  33 " - pdb=" SG  CYS D  42 " 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: 2.42
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 29 sheets defined
      12.0% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 32
      removed outlier: 3.605A  pdb=" N   PHE A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.852A  pdb=" N   LEU A  55 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A  56 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 56'
    Processing helix  chain 'A' and resid 88 through 91
      removed outlier: 3.853A  pdb=" N   ASN A  91 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 91'
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 4.119A  pdb=" N   SER A 137 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ILE A 138 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 134 through 138'
    Processing helix  chain 'A' and resid 147 through 151
      removed outlier: 4.417A  pdb=" N   SER A 150 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN A 151 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 147 through 151'
    Processing helix  chain 'A' and resid 203 through 207
      removed outlier: 4.118A  pdb=" N   CYS A 207 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 336
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.985A  pdb=" N   ASP A 369 " --> pdb=" O   GLN A 366 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE A 370 " --> pdb=" O   GLU A 367 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   THR A 373 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.603A  pdb=" N   GLU A 397 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 410
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 473 through 479
    Processing helix  chain 'A' and resid 495 through 499
      removed outlier: 3.747A  pdb=" N   CYS A 499 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 555
      removed outlier: 3.856A  pdb=" N   CYS A 555 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 29
      removed outlier: 3.760A  pdb=" N   PHE B  24 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.517A  pdb=" N   LEU B  55 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR B  57 " --> pdb=" O   PHE B  54 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE B  58 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 91
      removed outlier: 3.994A  pdb=" N   ASN B  91 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 91'
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.635A  pdb=" N   SER B 137 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE B 138 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 134 through 138'
    Processing helix  chain 'B' and resid 318 through 322
      removed outlier: 3.755A  pdb=" N   LYS B 322 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
    Processing helix  chain 'B' and resid 364 through 374
      removed outlier: 3.767A  pdb=" N   LEU B 368 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE B 370 " --> pdb=" O   GLU B 367 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   THR B 373 " --> pdb=" O   ILE B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 397
    Processing helix  chain 'B' and resid 407 through 410
    Processing helix  chain 'B' and resid 471 through 477
    Processing helix  chain 'B' and resid 495 through 499
      removed outlier: 3.815A  pdb=" N   CYS B 499 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 581
      removed outlier: 3.947A  pdb=" N   ASN B 580 " --> pdb=" O   GLY B 577 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42
      removed outlier: 6.225A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   ALA A  68 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   ARG A 125 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ALA A  96 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   SER A 127 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LEU A  98 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL A 124 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 246
    Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262
    Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 278
      removed outlier: 4.093A  pdb=" N   SER A 282 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 296
    Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.317A  pdb=" N   CYS A 313 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 347
      removed outlier: 6.238A  pdb=" N   LEU A 345 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ASP A 436 " --> pdb=" O   PHE A 412 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A 440 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 377
    Processing sheet with id=AB2, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.731A  pdb=" N   ILE A 532 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563
    Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 576
      removed outlier: 4.774A  pdb=" N   VAL A 575 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 583 " --> pdb=" O   VAL A 575 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 21 through 23
    Processing sheet with id=AB6, first strand: chain 'C' and resid 37 through 38
    Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 41 through 44
      removed outlier: 5.267A  pdb=" N   ALA B 123 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 246 through 247
      removed outlier: 3.787A  pdb=" N   GLN B 252 " --> pdb=" O   ASN B 247 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 261 through 263
    Processing sheet with id=AC2, first strand: chain 'B' and resid 276 through 277
    Processing sheet with id=AC3, first strand: chain 'B' and resid 291 through 296
    Processing sheet with id=AC4, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.589A  pdb=" N   CYS B 313 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 347
      removed outlier: 6.299A  pdb=" N   LEU B 345 " --> pdb=" O   LEU B 382 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU B 381 " --> pdb=" O   SER B 413 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   PHE B 412 " --> pdb=" O   ASP B 436 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE B 438 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LEU B 414 " --> pdb=" O   ILE B 438 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 505 through 506
      removed outlier: 3.572A  pdb=" N   VAL B 505 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 524 through 527
      removed outlier: 3.529A  pdb=" N   GLU B 527 " --> pdb=" O   GLU B 530 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 561 through 563
    Processing sheet with id=AC9, first strand: chain 'B' and resid 585 through 587
    Processing sheet with id=AD1, first strand: chain 'D' and resid 21 through 23
    Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38

    130 hydrogen bonds defined for protein.
    246 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: 3.19

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3424
        1.34 -     1.46: 1905
        1.46 -     1.58: 4937
        1.58 -     1.70: 0
        1.70 -     1.82: 156
  Bond restraints: 10422
  Sorted by residual:
  bond pdb=" N   CYS B 571 "
       pdb=" CA  CYS B 571 "
    ideal  model  delta    sigma   weight residual
    1.454  1.497 -0.043 1.14e-02 7.69e+03 1.40e+01
  bond pdb=" N   VAL A 481 "
       pdb=" CA  VAL A 481 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.11e-02 8.12e+03 1.23e+01
  bond pdb=" N   SER A  11 "
       pdb=" CA  SER A  11 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.044 1.29e-02 6.01e+03 1.17e+01
  bond pdb=" N   VAL B 500 "
       pdb=" CA  VAL B 500 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.10e-02 8.26e+03 1.05e+01
  bond pdb=" N   CYS A 482 "
       pdb=" CA  CYS A 482 "
    ideal  model  delta    sigma   weight residual
    1.453  1.494 -0.041 1.31e-02 5.83e+03 1.00e+01
  ... (remaining 10417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 13128
        1.39 -     2.77: 741
        2.77 -     4.16: 176
        4.16 -     5.55: 47
        5.55 -     6.93: 8
  Bond angle restraints: 14100
  Sorted by residual:
  angle pdb=" CA  HIS B 560 "
        pdb=" C   HIS B 560 "
        pdb=" N   TYR B 561 "
      ideal   model   delta    sigma   weight residual
     119.56  116.22    3.34 5.80e-01 2.97e+00 3.31e+01
  angle pdb=" N   SER B 169 "
        pdb=" CA  SER B 169 "
        pdb=" C   SER B 169 "
      ideal   model   delta    sigma   weight residual
     112.93  107.94    4.99 1.12e+00 7.97e-01 1.99e+01
  angle pdb=" N   VAL B 526 "
        pdb=" CA  VAL B 526 "
        pdb=" C   VAL B 526 "
      ideal   model   delta    sigma   weight residual
     107.75  114.08   -6.33 1.46e+00 4.69e-01 1.88e+01
  angle pdb=" CA  HIS C  16 "
        pdb=" C   HIS C  16 "
        pdb=" O   HIS C  16 "
      ideal   model   delta    sigma   weight residual
     122.64  117.27    5.37 1.25e+00 6.40e-01 1.84e+01
  angle pdb=" C   GLY B 564 "
        pdb=" N   PRO B 565 "
        pdb=" CA  PRO B 565 "
      ideal   model   delta    sigma   weight residual
     119.28  123.99   -4.71 1.10e+00 8.26e-01 1.83e+01
  ... (remaining 14095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 5742
       17.30 -    34.60: 575
       34.60 -    51.90: 123
       51.90 -    69.20: 23
       69.20 -    86.51: 17
  Dihedral angle restraints: 6480
    sinusoidal: 2692
      harmonic: 3788
  Sorted by residual:
  dihedral pdb=" CB  CYS B 287 "
           pdb=" SG  CYS B 287 "
           pdb=" SG  CYS B 302 "
           pdb=" CB  CYS B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.50  -82.50     1      1.00e+01 1.00e-02 8.35e+01
  dihedral pdb=" CB  CYS D  14 "
           pdb=" SG  CYS D  14 "
           pdb=" SG  CYS D  31 "
           pdb=" CB  CYS D  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.59  -70.59     1      1.00e+01 1.00e-02 6.41e+01
  dihedral pdb=" CB  CYS C  14 "
           pdb=" SG  CYS C  14 "
           pdb=" SG  CYS C  31 "
           pdb=" CB  CYS C  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.40  -59.40     1      1.00e+01 1.00e-02 4.71e+01
  ... (remaining 6477 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1136
       0.055 -    0.109: 330
       0.109 -    0.164: 55
       0.164 -    0.218: 8
       0.218 -    0.273: 5
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" CA  CYS B 596 "
            pdb=" N   CYS B 596 "
            pdb=" C   CYS B 596 "
            pdb=" CB  CYS B 596 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  SER A  11 "
            pdb=" N   SER A  11 "
            pdb=" C   SER A  11 "
            pdb=" CB  SER A  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LEU A 517 "
            pdb=" N   LEU A 517 "
            pdb=" C   LEU A 517 "
            pdb=" CB  LEU A 517 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1531 not shown)

  Planarity restraints: 1864
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  12 "    0.015 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ASN B  12 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASN B  12 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LYS B  13 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 168 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   PRO B 168 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PRO B 168 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 169 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 486 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.75e+00
        pdb=" C   CYS B 486 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   CYS B 486 "    0.014 2.00e-02 2.50e+03
        pdb=" N   SER B 487 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1861 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 531
        2.72 -     3.27: 10059
        3.27 -     3.81: 14845
        3.81 -     4.36: 19769
        4.36 -     4.90: 34034
  Nonbonded interactions: 79238
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 203 "
            pdb=" OD2 ASP A 206 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OD1 ASP B  51 "
            pdb=" OG  SER B  53 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG1 THR B 278 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OD1 ASP A  51 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE1 GLU A 118 "
            pdb=" NH2 ARG A 198 "
     model   vdw
     2.242 3.120
  ... (remaining 79233 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 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:             4.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.320
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10478  Z= 0.298
  Angle     :  0.804   8.799  14212  Z= 0.500
  Chirality :  0.053   0.273   1534
  Planarity :  0.004   0.042   1864
  Dihedral  : 14.456  86.506   3884
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 11.13 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  5.89 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.19), residues: 1314
  helix: -4.18 (0.31), residues: 67
  sheet: -3.56 (0.32), residues: 189
  loop : -2.96 (0.16), residues: 1058

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 492 
 HIS   0.004   0.001   HIS C  16 
 PHE   0.014   0.001   PHE A 380 
 TYR   0.012   0.001   TYR A  64 
 ARG   0.004   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29637 (  130)
  hydrogen bonds       : angle       9.84154 (  246)
  SS BOND              : bond        0.00798 (   56)
  SS BOND              : angle       2.10066 (  112)
  covalent geometry    : bond        0.00501 (10422)
  covalent geometry    : angle       0.78524 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  561 TYR cc_start: 0.8392 (m-80) cc_final: 0.8057 (m-80)
  outliers start: 20
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2968
  time to fit residues: 32.6666
Evaluate side-chains
  41 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  562 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A  70 ASN
A 100 ASN
A 128 ASN
A 194 GLN
A 209 HIS
A 252 GLN
A 394 HIS
** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 480 GLN
A 528 ASN
A 599 ASN
C  16 HIS
B 134 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
B 252 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 HIS
D  16 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.048686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.033875 restraints weight = 49655.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.2659 rms_B_bonded: 4.42
r_work: 0.2508 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2492 r_free = 0.2492    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10478  Z= 0.281
  Angle     :  0.709  16.310  14212  Z= 0.362
  Chirality :  0.049   0.172   1534
  Planarity :  0.004   0.040   1864
  Dihedral  :  5.534  37.688   1424
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.49 %
    Favored  : 88.47 %
  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: -3.42 (0.21), residues: 1314
  helix: -2.98 (0.48), residues: 75
  sheet: -3.05 (0.36), residues: 176
  loop : -2.28 (0.17), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 492 
 HIS   0.004   0.001   HIS B 483 
 PHE   0.008   0.001   PHE B 335 
 TYR   0.016   0.001   TYR B 561 
 ARG   0.005   0.000   ARG B 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  130)
  hydrogen bonds       : angle       6.39883 (  246)
  SS BOND              : bond        0.00663 (   56)
  SS BOND              : angle       1.24824 (  112)
  covalent geometry    : bond        0.00624 (10422)
  covalent geometry    : angle       0.70318 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 1.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9068 (p)
REVERT: A  152 MET cc_start: 0.9107 (mtp) cc_final: 0.8836 (mtp)
  outliers start: 12
  outliers final: 6
  residues processed: 46
  average time/residue: 0.2213
  time to fit residues: 18.2932
Evaluate side-chains
  42 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain D residue   17 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0970
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.049476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034683 restraints weight = 49797.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.2688 rms_B_bonded: 4.52
r_work: 0.2535 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2534 r_free = 0.2534    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2534 r_free = 0.2534    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10478  Z= 0.098
  Angle     :  0.565  10.602  14212  Z= 0.293
  Chirality :  0.045   0.163   1534
  Planarity :  0.003   0.040   1864
  Dihedral  :  4.849  18.235   1422
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.18 %
    Favored  : 87.09 %
  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: -2.80 (0.21), residues: 1314
  helix: -2.76 (0.49), residues: 80
  sheet: -2.67 (0.38), residues: 172
  loop : -1.79 (0.18), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 492 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.008   0.001   PHE A 380 
 TYR   0.011   0.001   TYR B 447 
 ARG   0.003   0.000   ARG B 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02900 (  130)
  hydrogen bonds       : angle       5.70806 (  246)
  SS BOND              : bond        0.00244 (   56)
  SS BOND              : angle       0.90397 (  112)
  covalent geometry    : bond        0.00222 (10422)
  covalent geometry    : angle       0.56155 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9030 (p)
REVERT: A   30 MET cc_start: 0.9725 (tpt) cc_final: 0.9505 (tpt)
REVERT: A  294 MET cc_start: 0.9163 (ptm) cc_final: 0.8652 (ppp)
  outliers start: 20
  outliers final: 11
  residues processed: 57
  average time/residue: 0.1573
  time to fit residues: 15.6569
Evaluate side-chains
  48 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain D residue   17 ASP
Chi-restraints excluded: chain D residue   19 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0040
   chunk 92 optimal weight:    0.9990
   chunk 123 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0570
   chunk 61 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5912

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

Flipped N/Q/H residues before XYZ refinement:
A 462 GLN
B 139 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.049658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.034947 restraints weight = 49073.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2704 rms_B_bonded: 4.49
r_work: 0.2552 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10478  Z= 0.094
  Angle     :  0.543   8.835  14212  Z= 0.279
  Chirality :  0.045   0.156   1534
  Planarity :  0.003   0.040   1864
  Dihedral  :  4.534  18.703   1422
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.70 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.22), residues: 1314
  helix: -2.51 (0.53), residues: 80
  sheet: -2.32 (0.40), residues: 168
  loop : -1.50 (0.18), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 492 
 HIS   0.002   0.000   HIS B 121 
 PHE   0.010   0.001   PHE A 380 
 TYR   0.009   0.001   TYR B 447 
 ARG   0.003   0.000   ARG B 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02498 (  130)
  hydrogen bonds       : angle       5.43323 (  246)
  SS BOND              : bond        0.00210 (   56)
  SS BOND              : angle       0.80498 (  112)
  covalent geometry    : bond        0.00216 (10422)
  covalent geometry    : angle       0.54011 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.8988 (p)
REVERT: B  244 MET cc_start: 0.9701 (mmp) cc_final: 0.9485 (mmp)
  outliers start: 19
  outliers final: 12
  residues processed: 54
  average time/residue: 0.1503
  time to fit residues: 14.1650
Evaluate side-chains
  48 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   17 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0470
   chunk 121 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 60 optimal weight:   20.0000
   chunk 105 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.048661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.034069 restraints weight = 49764.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 4.52
r_work: 0.2522 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2520 r_free = 0.2520    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2520 r_free = 0.2520    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10478  Z= 0.150
  Angle     :  0.569   7.312  14212  Z= 0.291
  Chirality :  0.046   0.159   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.598  18.492   1422
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.87 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.22), residues: 1314
  helix: -2.26 (0.55), residues: 80
  sheet: -2.26 (0.41), residues: 160
  loop : -1.30 (0.19), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 140 
 HIS   0.002   0.000   HIS A 209 
 PHE   0.010   0.001   PHE A 380 
 TYR   0.010   0.001   TYR B 447 
 ARG   0.002   0.000   ARG B 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02604 (  130)
  hydrogen bonds       : angle       5.43398 (  246)
  SS BOND              : bond        0.00289 (   56)
  SS BOND              : angle       0.86926 (  112)
  covalent geometry    : bond        0.00339 (10422)
  covalent geometry    : angle       0.56608 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 38
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9034 (p)
REVERT: A  152 MET cc_start: 0.9301 (ttm) cc_final: 0.9023 (mtp)
REVERT: B  154 MET cc_start: 0.9123 (mmm) cc_final: 0.8556 (mmp)
REVERT: B  244 MET cc_start: 0.9698 (mmp) cc_final: 0.9424 (mmm)
REVERT: B  543 MET cc_start: 0.8041 (ppp) cc_final: 0.7822 (tmm)
  outliers start: 24
  outliers final: 16
  residues processed: 59
  average time/residue: 0.1913
  time to fit residues: 18.4667
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 35
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.048975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.034477 restraints weight = 49599.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 4.52
r_work: 0.2542 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2541 r_free = 0.2541    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2541 r_free = 0.2541    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10478  Z= 0.106
  Angle     :  0.546   7.156  14212  Z= 0.280
  Chirality :  0.045   0.159   1534
  Planarity :  0.003   0.042   1864
  Dihedral  :  4.455  18.328   1422
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.32 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.74 %
    Favored  : 85.18 %
  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: -1.97 (0.23), residues: 1314
  helix: -2.20 (0.55), residues: 80
  sheet: -2.21 (0.41), residues: 160
  loop : -1.16 (0.19), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 140 
 HIS   0.002   0.000   HIS B 121 
 PHE   0.009   0.001   PHE A 380 
 TYR   0.010   0.001   TYR B 447 
 ARG   0.002   0.000   ARG B 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02289 (  130)
  hydrogen bonds       : angle       5.26971 (  246)
  SS BOND              : bond        0.00229 (   56)
  SS BOND              : angle       0.81013 (  112)
  covalent geometry    : bond        0.00246 (10422)
  covalent geometry    : angle       0.54327 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9023 (p)
REVERT: B  154 MET cc_start: 0.9125 (mmm) cc_final: 0.8697 (mmp)
REVERT: B  244 MET cc_start: 0.9694 (mmp) cc_final: 0.9408 (mmm)
  outliers start: 24
  outliers final: 17
  residues processed: 62
  average time/residue: 0.1803
  time to fit residues: 17.8528
Evaluate side-chains
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 35
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 117 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0770
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    2.4146

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

Flipped N/Q/H residues before XYZ refinement:
B  23 HIS
B  70 ASN
B 129 ASN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.047998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.033304 restraints weight = 51224.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 4.48
r_work: 0.2504 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2504 r_free = 0.2504    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2504 r_free = 0.2504    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  10478  Z= 0.247
  Angle     :  0.641   7.870  14212  Z= 0.327
  Chirality :  0.047   0.197   1534
  Planarity :  0.003   0.043   1864
  Dihedral  :  4.903  20.746   1422
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.69 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.34 %
    Favored  : 84.84 %
  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: -1.90 (0.23), residues: 1314
  helix: -1.95 (0.56), residues: 81
  sheet: -2.26 (0.40), residues: 174
  loop : -1.09 (0.19), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 140 
 HIS   0.003   0.001   HIS B 535 
 PHE   0.010   0.001   PHE B 126 
 TYR   0.011   0.001   TYR B 447 
 ARG   0.003   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  130)
  hydrogen bonds       : angle       5.45091 (  246)
  SS BOND              : bond        0.00420 (   56)
  SS BOND              : angle       1.13172 (  112)
  covalent geometry    : bond        0.00557 (10422)
  covalent geometry    : angle       0.63552 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9012 (p)
REVERT: B  244 MET cc_start: 0.9666 (mmp) cc_final: 0.9344 (mmm)
REVERT: B  505 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7037 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 55
  average time/residue: 0.1601
  time to fit residues: 15.5130
Evaluate side-chains
  54 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 35
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   19 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 120 optimal weight:    0.0270
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.048948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.034278 restraints weight = 50376.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.2698 rms_B_bonded: 4.48
r_work: 0.2545 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2547 r_free = 0.2547    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2547 r_free = 0.2547    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10478  Z= 0.102
  Angle     :  0.571   9.034  14212  Z= 0.291
  Chirality :  0.045   0.192   1534
  Planarity :  0.003   0.045   1864
  Dihedral  :  4.539  19.236   1422
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.94 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.52 %
    Favored  : 84.84 %
  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: -1.77 (0.23), residues: 1314
  helix: -1.87 (0.57), residues: 81
  sheet: -2.13 (0.40), residues: 169
  loop : -1.01 (0.19), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 140 
 HIS   0.002   0.000   HIS B 121 
 PHE   0.009   0.001   PHE A 380 
 TYR   0.009   0.001   TYR A 292 
 ARG   0.002   0.000   ARG B 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02242 (  130)
  hydrogen bonds       : angle       5.18313 (  246)
  SS BOND              : bond        0.00245 (   56)
  SS BOND              : angle       0.85656 (  112)
  covalent geometry    : bond        0.00238 (10422)
  covalent geometry    : angle       0.56820 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9027 (p)
REVERT: A  294 MET cc_start: 0.8800 (pmm) cc_final: 0.8380 (pmm)
  outliers start: 19
  outliers final: 17
  residues processed: 56
  average time/residue: 0.1643
  time to fit residues: 15.9270
Evaluate side-chains
  55 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0370
   chunk 82 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0470
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.049323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.034776 restraints weight = 50233.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 4.47
r_work: 0.2570 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10478  Z= 0.093
  Angle     :  0.577  13.145  14212  Z= 0.290
  Chirality :  0.045   0.237   1534
  Planarity :  0.003   0.045   1864
  Dihedral  :  4.378  18.637   1422
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.62 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.21 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.23), residues: 1314
  helix: -1.80 (0.56), residues: 81
  sheet: -2.07 (0.40), residues: 169
  loop : -0.96 (0.19), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 140 
 HIS   0.002   0.000   HIS A 346 
 PHE   0.010   0.001   PHE A 380 
 TYR   0.009   0.001   TYR B 447 
 ARG   0.002   0.000   ARG B 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02091 (  130)
  hydrogen bonds       : angle       5.18493 (  246)
  SS BOND              : bond        0.00204 (   56)
  SS BOND              : angle       0.77247 (  112)
  covalent geometry    : bond        0.00219 (10422)
  covalent geometry    : angle       0.57558 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9024 (p)
REVERT: A  154 MET cc_start: 0.8794 (mpp) cc_final: 0.8535 (mpp)
REVERT: A  244 MET cc_start: 0.9108 (mtp) cc_final: 0.8543 (mmm)
REVERT: A  294 MET cc_start: 0.8866 (pmm) cc_final: 0.8431 (pmm)
REVERT: D   46 ASP cc_start: 0.9432 (t0) cc_final: 0.8974 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 54
  average time/residue: 0.1908
  time to fit residues: 18.1312
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 126 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.048793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.034089 restraints weight = 51023.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2695 rms_B_bonded: 4.51
r_work: 0.2545 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10478  Z= 0.149
  Angle     :  0.611  13.715  14212  Z= 0.303
  Chirality :  0.046   0.235   1534
  Planarity :  0.003   0.044   1864
  Dihedral  :  4.491  19.535   1422
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.85 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.38 %
    Favored  : 84.32 %
  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: -1.60 (0.23), residues: 1314
  helix: -1.54 (0.58), residues: 81
  sheet: -2.03 (0.40), residues: 167
  loop : -0.91 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 140 
 HIS   0.002   0.001   HIS A 209 
 PHE   0.009   0.001   PHE A 380 
 TYR   0.009   0.001   TYR B 447 
 ARG   0.002   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02359 (  130)
  hydrogen bonds       : angle       5.19612 (  246)
  SS BOND              : bond        0.00282 (   56)
  SS BOND              : angle       0.88065 (  112)
  covalent geometry    : bond        0.00344 (10422)
  covalent geometry    : angle       0.60799 (14100)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9021 (p)
REVERT: A  154 MET cc_start: 0.8559 (mpp) cc_final: 0.8317 (mpp)
REVERT: A  294 MET cc_start: 0.8929 (pmm) cc_final: 0.8470 (pmm)
REVERT: B  344 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8474 (m-30)
  outliers start: 15
  outliers final: 13
  residues processed: 52
  average time/residue: 0.1720
  time to fit residues: 16.0105
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  191 CYS
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 78 optimal weight:    0.0470
   chunk 90 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 99 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.049530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034944 restraints weight = 50376.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 4.47
r_work: 0.2580 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10478  Z= 0.091
  Angle     :  0.573  12.982  14212  Z= 0.287
  Chirality :  0.045   0.232   1534
  Planarity :  0.003   0.043   1864
  Dihedral  :  4.264  18.451   1422
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.16 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.47 %
    Favored  : 84.23 %
  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: -1.54 (0.23), residues: 1314
  helix: -1.49 (0.58), residues: 81
  sheet: -2.06 (0.40), residues: 164
  loop : -0.85 (0.19), residues: 1069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 492 
 HIS   0.002   0.000   HIS A 346 
 PHE   0.010   0.001   PHE A 380 
 TYR   0.009   0.001   TYR B 447 
 ARG   0.002   0.000   ARG B 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02078 (  130)
  hydrogen bonds       : angle       5.04568 (  246)
  SS BOND              : bond        0.00199 (   56)
  SS BOND              : angle       0.74741 (  112)
  covalent geometry    : bond        0.00215 (10422)
  covalent geometry    : angle       0.57141 (14100)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5384.58 seconds
wall clock time: 94 minutes 23.29 seconds (5663.29 seconds total)