Starting phenix.real_space_refine
on Thu Mar  5 02:25:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_25558.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_25558.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_25558.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_25558.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sz0_25558/03_2026/7sz0_25558.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.42, per 1000 atoms: 0.24
  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: 0.78
  Conformation dependent library (CDL) restraints added in 474.0 milliseconds
  

  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: 0.37
  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: 1.49

  Time building geometry restraints manager: 1.10 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: 0.02
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:             2.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.910
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.900
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.000   ARG A 503 
 TYR   0.012   0.001   TYR A  64 
 PHE   0.014   0.001   PHE A 380 
 TRP   0.011   0.001   TRP A 492 
 HIS   0.004   0.001   HIS C  16 

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

*********************** 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  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  561 TYR cc_start: 0.8392 (m-80) cc_final: 0.8056 (m-80)
  outliers start: 20
  outliers final: 3
  residues processed: 75
  average time/residue: 0.0979
  time to fit residues: 10.8997
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  : 0.434 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0670
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.0030
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0370
   chunk 129 optimal weight:    1.9990
   overall best weight:    0.8210

-------------------------------------------------------------------------------
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 599 ASN
C  16 HIS
B  70 ASN
B 134 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
B 252 GLN
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 = 0.3248 r_free = 0.3248 target = 0.050565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035734 restraints weight = 49296.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 4.48
r_work: 0.2574 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2563 r_free = 0.2563    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2557 r_free = 0.2557    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10478  Z= 0.121
  Angle     :  0.618  15.262  14212  Z= 0.317
  Chirality :  0.046   0.173   1534
  Planarity :  0.004   0.040   1864
  Dihedral  :  5.108  35.182   1424
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.14 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.21), residues: 1314
  helix: -3.33 (0.42), residues: 80
  sheet: -2.98 (0.36), residues: 172
  loop : -2.19 (0.17), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 509 
 TYR   0.012   0.001   TYR B 447 
 PHE   0.007   0.001   PHE A 380 
 TRP   0.009   0.001   TRP A 492 
 HIS   0.004   0.001   HIS B 594 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10422)
  covalent geometry    : angle       0.61462 (14100)
  SS BOND              : bond        0.00246 (   56)
  SS BOND              : angle       0.98093 (  112)
  hydrogen bonds       : bond        0.03470 (  130)
  hydrogen bonds       : angle       6.17704 (  246)

*********************** 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: 10
    poor density    : 40
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9104 (p)
REVERT: A  152 MET cc_start: 0.9096 (mtp) cc_final: 0.8850 (mtp)
REVERT: C   27 ASP cc_start: 0.9391 (m-30) cc_final: 0.9191 (t0)
REVERT: B  244 MET cc_start: 0.9715 (mmp) cc_final: 0.9368 (mmp)
  outliers start: 10
  outliers final: 4
  residues processed: 47
  average time/residue: 0.0677
  time to fit residues: 5.5525
Evaluate side-chains
  41 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
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 99 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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  12 ASN
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 = 0.3234 r_free = 0.3234 target = 0.049862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.035060 restraints weight = 49541.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 4.50
r_work: 0.2566 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.1767

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= 0.111
  Angle     :  0.555   9.184  14212  Z= 0.288
  Chirality :  0.045   0.153   1534
  Planarity :  0.003   0.040   1864
  Dihedral  :  4.693  18.676   1422
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.44 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.21), residues: 1314
  helix: -2.80 (0.48), residues: 80
  sheet: -2.68 (0.38), residues: 162
  loop : -1.74 (0.18), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 509 
 TYR   0.012   0.001   TYR B 447 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.005   0.001   TRP A 492 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10422)
  covalent geometry    : angle       0.55135 (14100)
  SS BOND              : bond        0.00236 (   56)
  SS BOND              : angle       0.89796 (  112)
  hydrogen bonds       : bond        0.02927 (  130)
  hydrogen bonds       : angle       5.69188 (  246)

*********************** 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
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9038 (p)
REVERT: A   30 MET cc_start: 0.9732 (tpt) cc_final: 0.9526 (tpt)
REVERT: A  283 CYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8365 (m)
REVERT: A  294 MET cc_start: 0.9220 (ptm) cc_final: 0.8659 (ppp)
REVERT: C   21 MET cc_start: 0.8916 (ptp) cc_final: 0.8637 (ptp)
REVERT: C   27 ASP cc_start: 0.9422 (m-30) cc_final: 0.9195 (t0)
REVERT: B  244 MET cc_start: 0.9728 (mmp) cc_final: 0.9322 (mmp)
  outliers start: 13
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0628
  time to fit residues: 5.6797
Evaluate side-chains
  44 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  283 CYS
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
Chi-restraints excluded: chain D residue   31 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 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 = 0.3218 r_free = 0.3218 target = 0.049158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.034503 restraints weight = 49557.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 4.51
r_work: 0.2534 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2534
-------------------------------------------------------------------------------
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 = 0.88   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 = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2047

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= 0.125
  Angle     :  0.549   8.486  14212  Z= 0.283
  Chirality :  0.045   0.159   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.560  18.647   1422
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.44 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.22), residues: 1314
  helix: -2.45 (0.54), residues: 80
  sheet: -2.31 (0.40), residues: 168
  loop : -1.48 (0.18), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 509 
 TYR   0.010   0.001   TYR B 447 
 PHE   0.010   0.001   PHE A 380 
 TRP   0.007   0.001   TRP A 140 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10422)
  covalent geometry    : angle       0.54573 (14100)
  SS BOND              : bond        0.00252 (   56)
  SS BOND              : angle       0.83797 (  112)
  hydrogen bonds       : bond        0.02566 (  130)
  hydrogen bonds       : angle       5.48487 (  246)

*********************** 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
  65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9033 (p)
REVERT: A  283 CYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8382 (m)
REVERT: C   21 MET cc_start: 0.8847 (ptp) cc_final: 0.8566 (ptp)
REVERT: C   27 ASP cc_start: 0.9463 (m-30) cc_final: 0.9206 (t0)
REVERT: B  244 MET cc_start: 0.9725 (mmp) cc_final: 0.9275 (mmp)
  outliers start: 26
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0661
  time to fit residues: 6.8417
Evaluate side-chains
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  283 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  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  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 90 optimal weight:    0.0770
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 120 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0070
   chunk 42 optimal weight:    0.0010
   chunk 124 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 44 optimal weight:    0.2980
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.1962

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.050376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.035626 restraints weight = 49596.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 4.51
r_work: 0.2599 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10478  Z= 0.081
  Angle     :  0.530   7.595  14212  Z= 0.271
  Chirality :  0.044   0.150   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.252  17.711   1422
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.82 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.22), residues: 1314
  helix: -2.35 (0.54), residues: 80
  sheet: -2.26 (0.41), residues: 153
  loop : -1.28 (0.18), residues: 1081

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 (10422)
  covalent geometry    : angle       0.52859 (14100)
  SS BOND              : bond        0.00185 (   56)
  SS BOND              : angle       0.70848 (  112)
  hydrogen bonds       : bond        0.02154 (  130)
  hydrogen bonds       : angle       5.32930 (  246)

*********************** 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
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9012 (p)
REVERT: A  244 MET cc_start: 0.9328 (mtp) cc_final: 0.8885 (mmm)
REVERT: A  294 MET cc_start: 0.9389 (ptt) cc_final: 0.9184 (ptt)
REVERT: C   21 MET cc_start: 0.8859 (ptp) cc_final: 0.8563 (ptp)
REVERT: C   27 ASP cc_start: 0.9460 (m-30) cc_final: 0.9190 (t0)
REVERT: C   46 ASP cc_start: 0.9377 (t0) cc_final: 0.9078 (t0)
REVERT: B  244 MET cc_start: 0.9710 (mmp) cc_final: 0.9245 (mmp)
REVERT: B  505 VAL cc_start: 0.7358 (OUTLIER) cc_final: 0.6853 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0789
  time to fit residues: 7.1349
Evaluate side-chains
  50 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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  604 CYS
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0030
   chunk 63 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 462 GLN
** 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 = 0.3244 r_free = 0.3244 target = 0.049939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035245 restraints weight = 50101.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 4.51
r_work: 0.2568 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    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 = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10478  Z= 0.095
  Angle     :  0.526   7.653  14212  Z= 0.269
  Chirality :  0.044   0.153   1534
  Planarity :  0.003   0.043   1864
  Dihedral  :  4.216  17.218   1422
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.00 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.23), residues: 1314
  helix: -2.14 (0.57), residues: 80
  sheet: -2.04 (0.44), residues: 143
  loop : -1.15 (0.19), residues: 1091

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10422)
  covalent geometry    : angle       0.52359 (14100)
  SS BOND              : bond        0.00208 (   56)
  SS BOND              : angle       0.74614 (  112)
  hydrogen bonds       : bond        0.02251 (  130)
  hydrogen bonds       : angle       5.20288 (  246)

*********************** 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
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8988 (p)
REVERT: A   30 MET cc_start: 0.9673 (tpt) cc_final: 0.9382 (tpt)
REVERT: A  244 MET cc_start: 0.9306 (mtp) cc_final: 0.8738 (mmm)
REVERT: C   21 MET cc_start: 0.8818 (ptp) cc_final: 0.8526 (ptp)
REVERT: C   27 ASP cc_start: 0.9463 (m-30) cc_final: 0.9180 (t0)
REVERT: C   46 ASP cc_start: 0.9389 (t0) cc_final: 0.9084 (t0)
REVERT: B  244 MET cc_start: 0.9688 (mmp) cc_final: 0.9207 (mmp)
  outliers start: 17
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0711
  time to fit residues: 6.4254
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  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  154 MET
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  464 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0970
   chunk 33 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3243 r_free = 0.3243 target = 0.049861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.035198 restraints weight = 49765.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 4.50
r_work: 0.2582 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10478  Z= 0.099
  Angle     :  0.534   8.286  14212  Z= 0.272
  Chirality :  0.045   0.186   1534
  Planarity :  0.003   0.043   1864
  Dihedral  :  4.178  17.566   1422
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.16 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.34 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.23), residues: 1314
  helix: -2.06 (0.57), residues: 80
  sheet: -2.06 (0.42), residues: 153
  loop : -1.04 (0.19), residues: 1081

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10422)
  covalent geometry    : angle       0.53145 (14100)
  SS BOND              : bond        0.00207 (   56)
  SS BOND              : angle       0.75077 (  112)
  hydrogen bonds       : bond        0.02151 (  130)
  hydrogen bonds       : angle       5.11713 (  246)

*********************** 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
  55 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9001 (p)
REVERT: A   30 MET cc_start: 0.9654 (tpt) cc_final: 0.9377 (tpt)
REVERT: A  244 MET cc_start: 0.9306 (mtp) cc_final: 0.8747 (mmm)
REVERT: C   21 MET cc_start: 0.8809 (ptp) cc_final: 0.8519 (ptp)
REVERT: C   27 ASP cc_start: 0.9474 (m-30) cc_final: 0.9161 (t0)
REVERT: C   46 ASP cc_start: 0.9377 (t0) cc_final: 0.9068 (t0)
REVERT: B  244 MET cc_start: 0.9692 (mmp) cc_final: 0.9402 (mmm)
  outliers start: 14
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0761
  time to fit residues: 7.0327
Evaluate side-chains
  52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
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 C residue   31 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  464 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 528 ASN
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 = 0.3205 r_free = 0.3205 target = 0.048626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.033874 restraints weight = 50364.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2677 rms_B_bonded: 4.49
r_work: 0.2522 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2524 r_free = 0.2524    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 = 0.2524 r_free = 0.2524    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10478  Z= 0.196
  Angle     :  0.605  12.229  14212  Z= 0.306
  Chirality :  0.046   0.232   1534
  Planarity :  0.003   0.041   1864
  Dihedral  :  4.570  20.091   1422
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.16 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.23), residues: 1314
  helix: -1.78 (0.59), residues: 80
  sheet: -2.01 (0.40), residues: 169
  loop : -0.98 (0.19), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.010   0.001   TYR B 447 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.007   0.001   TRP C  49 
 HIS   0.003   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10422)
  covalent geometry    : angle       0.60034 (14100)
  SS BOND              : bond        0.00352 (   56)
  SS BOND              : angle       1.00366 (  112)
  hydrogen bonds       : bond        0.02566 (  130)
  hydrogen bonds       : angle       5.25608 (  246)

*********************** 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
  55 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9023 (p)
REVERT: A   30 MET cc_start: 0.9698 (tpt) cc_final: 0.9350 (tpt)
REVERT: A  244 MET cc_start: 0.9229 (mtp) cc_final: 0.8604 (mmm)
REVERT: A  294 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8306 (pmm)
REVERT: C   21 MET cc_start: 0.8780 (ptp) cc_final: 0.8502 (ptp)
REVERT: C   27 ASP cc_start: 0.9483 (m-30) cc_final: 0.9172 (t0)
REVERT: B  244 MET cc_start: 0.9625 (mmp) cc_final: 0.9383 (mmm)
  outliers start: 15
  outliers final: 13
  residues processed: 54
  average time/residue: 0.0707
  time to fit residues: 6.6455
Evaluate side-chains
  53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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  294 MET
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  562 ILE
Chi-restraints excluded: chain D residue   19 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.049225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.034471 restraints weight = 50120.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 4.50
r_work: 0.2555 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    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 = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10478  Z= 0.108
  Angle     :  0.563  10.846  14212  Z= 0.285
  Chirality :  0.045   0.216   1534
  Planarity :  0.003   0.042   1864
  Dihedral  :  4.344  19.192   1422
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.09 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.86 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.23), residues: 1314
  helix: -1.69 (0.59), residues: 80
  sheet: -1.87 (0.42), residues: 159
  loop : -0.90 (0.19), residues: 1075

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.008   0.001   PHE A 380 
 TRP   0.005   0.001   TRP B 140 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10422)
  covalent geometry    : angle       0.56032 (14100)
  SS BOND              : bond        0.00236 (   56)
  SS BOND              : angle       0.80190 (  112)
  hydrogen bonds       : bond        0.02195 (  130)
  hydrogen bonds       : angle       5.13745 (  246)

*********************** 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
  55 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9026 (p)
REVERT: A   30 MET cc_start: 0.9708 (tpt) cc_final: 0.9387 (tpt)
REVERT: A  244 MET cc_start: 0.9197 (mtp) cc_final: 0.8572 (mmm)
REVERT: A  294 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8408 (pmm)
REVERT: C   21 MET cc_start: 0.8734 (ptp) cc_final: 0.8446 (ptp)
REVERT: C   27 ASP cc_start: 0.9485 (m-30) cc_final: 0.9165 (t0)
REVERT: B  244 MET cc_start: 0.9696 (mmp) cc_final: 0.9399 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0698
  time to fit residues: 6.4574
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  : 0.433 
-------------------------------------------------------------------------------
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  294 MET
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  464 THR
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 14 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 109 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.048921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.034238 restraints weight = 49756.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 4.46
r_work: 0.2550 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10478  Z= 0.138
  Angle     :  0.583  10.730  14212  Z= 0.293
  Chirality :  0.045   0.220   1534
  Planarity :  0.003   0.042   1864
  Dihedral  :  4.382  19.603   1422
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.70 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.23), residues: 1314
  helix: -1.48 (0.60), residues: 80
  sheet: -1.81 (0.42), residues: 157
  loop : -0.82 (0.19), residues: 1077

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 198 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.007   0.001   TRP C  49 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10422)
  covalent geometry    : angle       0.58037 (14100)
  SS BOND              : bond        0.00272 (   56)
  SS BOND              : angle       0.85201 (  112)
  hydrogen bonds       : bond        0.02302 (  130)
  hydrogen bonds       : angle       5.17217 (  246)

********************** 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
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9009 (p)
REVERT: A   30 MET cc_start: 0.9708 (tpt) cc_final: 0.9384 (tpt)
REVERT: A  294 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8356 (pmm)
REVERT: C   21 MET cc_start: 0.8755 (ptp) cc_final: 0.8470 (ptp)
REVERT: C   27 ASP cc_start: 0.9477 (m-30) cc_final: 0.9189 (t0)
REVERT: B  233 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8982 (pp20)
REVERT: B  244 MET cc_start: 0.9696 (mmp) cc_final: 0.9402 (mmm)
  outliers start: 17
  outliers final: 14
  residues processed: 55
  average time/residue: 0.0724
  time to fit residues: 6.9375
Evaluate side-chains
  56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
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  294 MET
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  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 34 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0030
   chunk 39 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0570
   chunk 10 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.3908

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.049767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.035179 restraints weight = 49897.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.2737 rms_B_bonded: 4.48
r_work: 0.2586 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10478  Z= 0.087
  Angle     :  0.562  11.058  14212  Z= 0.282
  Chirality :  0.045   0.216   1534
  Planarity :  0.003   0.043   1864
  Dihedral  :  4.156  18.487   1422
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.63 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.23), residues: 1314
  helix: -1.43 (0.60), residues: 80
  sheet: -1.86 (0.42), residues: 154
  loop : -0.78 (0.19), residues: 1080

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.009   0.001   TYR B 447 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.006   0.001   TRP A 492 
 HIS   0.002   0.000   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 (10422)
  covalent geometry    : angle       0.56016 (14100)
  SS BOND              : bond        0.00187 (   56)
  SS BOND              : angle       0.72303 (  112)
  hydrogen bonds       : bond        0.02020 (  130)
  hydrogen bonds       : angle       5.01366 (  246)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2370.87 seconds
wall clock time: 41 minutes 24.21 seconds (2484.21 seconds total)