Starting phenix.real_space_refine
on Tue Jan 21 11:13:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vjc_43280/01_2025/8vjc_43280_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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 3397 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     111      5.16       5
     C    8843      2.51       5
     N    2402      2.21       5
     O    2571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13927
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6386
          Classifications: {'peptide': 787}
          Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 745}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 6495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 802, 6495
          Classifications: {'peptide': 802}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 758}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 323
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 420
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 2, 'TRANS': 51}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 303
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
          Chain breaks: 1
  Time building chain proxies: 8.20, per 1000 atoms: 0.59
  Number of scatterers: 13927
  At special positions: 0
  Unit cell: (117.72, 132.84, 185.76, 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     111     16.00
     O    2571      8.00
     N    2402      7.00
     C    8843      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=41, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - 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 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 304 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 647 " - pdb=" SG  CYS A 860 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 786 " - pdb=" SG  CYS A 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 155 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - 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 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS B 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 266 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 312 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 435 " - pdb=" SG  CYS B 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 647 " - pdb=" SG  CYS B 860 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 786 " - pdb=" SG  CYS B 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   9 " - pdb=" SG  CYS C  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  21 " - pdb=" SG  CYS C  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   9 " - pdb=" SG  CYS D  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  21 " - pdb=" SG  CYS D  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  46 " - pdb=" SG  CYS D  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   9 " - pdb=" SG  CYS E  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  46 " - pdb=" SG  CYS E  51 " distance=2.03

  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: 3.09
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3250

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 29 sheets defined
      15.2% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 26
      removed outlier: 4.147A  pdb=" N   ASN A  25 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS A  26 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 323 through 329
      removed outlier: 4.246A  pdb=" N   GLU A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 358
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.056A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU A 443 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 644
      removed outlier: 3.574A  pdb=" N   LEU A 641 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 644 " --> pdb=" O   LEU A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 714
      removed outlier: 3.760A  pdb=" N   LEU A 696 " --> pdb=" O   ILE A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 870
    Processing helix  chain 'B' and resid 16 through 24
      removed outlier: 3.888A  pdb=" N   ARG B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   HIS B  21 " --> pdb=" O   THR B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 47
      removed outlier: 3.613A  pdb=" N   PHE B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 143
      removed outlier: 3.547A  pdb=" N   ASP B 142 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
      removed outlier: 4.002A  pdb=" N   ASN B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 256 through 269
    Processing helix  chain 'B' and resid 323 through 328
    Processing helix  chain 'B' and resid 329 through 331
      No H-bonds generated for 'chain 'B' and resid 329 through 331'
    Processing helix  chain 'B' and resid 350 through 358
    Processing helix  chain 'B' and resid 435 through 446
      removed outlier: 3.739A  pdb=" N   ILE B 439 " --> pdb=" O   CYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 452
      removed outlier: 4.021A  pdb=" N   GLN B 452 " --> pdb=" O   LYS B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 643
    Processing helix  chain 'B' and resid 702 through 715
      removed outlier: 4.013A  pdb=" N   GLU B 706 " --> pdb=" O   ARG B 702 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASP B 707 " --> pdb=" O   LYS B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 863 through 869
    Processing helix  chain 'C' and resid 13 through 22
      removed outlier: 3.619A  pdb=" N   CYS C  21 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 60
      removed outlier: 3.722A  pdb=" N   CYS C  60 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 17
      removed outlier: 4.136A  pdb=" N   ASP D  15 " --> pdb=" O   GLY D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 47
    Processing helix  chain 'D' and resid 52 through 58
      removed outlier: 3.742A  pdb=" N   LEU D  56 " --> pdb=" O   ASP D  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 22
      removed outlier: 3.964A  pdb=" N   ASP E  15 " --> pdb=" O   GLY E  11 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR E  16 " --> pdb=" O   GLU E  12 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY E  22 " --> pdb=" O   GLN E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 59
      removed outlier: 3.971A  pdb=" N   THR E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 5.967A  pdb=" N   HIS A  32 " --> pdb=" O   PRO A   9 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A  34 " --> pdb=" O   MET A  11 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A  36 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13
      removed outlier: 5.967A  pdb=" N   HIS A  32 " --> pdb=" O   PRO A   9 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A  34 " --> pdb=" O   MET A  11 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A  36 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   MET A  98 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ARG A  65 " --> pdb=" O   MET A  98 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   ARG A 118 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A  94 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   GLU A 120 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   PHE A  96 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ASN A 122 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   MET A  98 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   TYR A 144 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248
    Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280
    Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313
      removed outlier: 3.827A  pdb=" N   ILE A 364 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321
      removed outlier: 7.689A  pdb=" N   PHE A 427 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   TYR A 401 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   HIS A 429 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A 403 " --> pdb=" O   HIS A 429 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480
      removed outlier: 3.558A  pdb=" N   TYR A 477 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A 488 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 479 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534
      removed outlier: 4.193A  pdb=" N   GLY A 502 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605
      removed outlier: 6.825A  pdb=" N   LYS A 614 " --> pdb=" O   PRO A 601 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   SER A 603 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE A 612 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762
    Processing sheet with id=AB4, first strand: chain 'A' and resid 819 through 822
    Processing sheet with id=AB5, first strand: chain 'A' and resid 856 through 862
      removed outlier: 3.661A  pdb=" N   LEU A 844 " --> pdb=" O   THR A 889 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 880 through 882
      removed outlier: 3.564A  pdb=" N   PHE A 903 " --> pdb=" O   TYR A 882 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.525A  pdb=" N   MET B  11 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   LEU B  36 " --> pdb=" O   MET B  11 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   ILE B  13 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   MET B  38 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE B  64 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B  66 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL B 117 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL B 146 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE B 119 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29
    Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173
    Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248
    Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279
    Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 294
    Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321
      removed outlier: 3.965A  pdb=" N   LEU B 314 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   SER B 339 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 8.905A  pdb=" N   GLU B 316 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 10.555A  pdb=" N   ILE B 341 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
      removed outlier: 9.880A  pdb=" N   GLU B 318 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ILE B 336 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLY B 366 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY B 338 " --> pdb=" O   GLY B 366 " (cutoff:3.500A)
      removed outlier: 11.039A  pdb=" N   GLU B 363 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 10.161A  pdb=" N   GLU B 391 " --> pdb=" O   GLU B 363 " (cutoff:3.500A)
      removed outlier: 9.001A  pdb=" N   SER B 365 " --> pdb=" O   GLU B 391 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321
      removed outlier: 3.965A  pdb=" N   LEU B 314 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   SER B 339 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 8.905A  pdb=" N   GLU B 316 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 10.555A  pdb=" N   ILE B 341 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
      removed outlier: 9.880A  pdb=" N   GLU B 318 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 9.054A  pdb=" N   LYS B 369 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU B 340 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ARG B 371 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ILE B 342 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   PHE B 427 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   TYR B 401 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   HIS B 429 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LEU B 403 " --> pdb=" O   HIS B 429 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 475 through 479
    Processing sheet with id=AC7, first strand: chain 'B' and resid 530 through 533
      removed outlier: 3.503A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 604
      removed outlier: 6.809A  pdb=" N   LYS B 614 " --> pdb=" O   PRO B 601 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   SER B 603 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE B 612 " --> pdb=" O   SER B 603 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762
      removed outlier: 3.603A  pdb=" N   GLU B 760 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B 630 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 819 through 822
    Processing sheet with id=AD2, first strand: chain 'B' and resid 856 through 862

    323 hydrogen bonds defined for protein.
    813 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: 5.04

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4562
        1.35 -     1.46: 3384
        1.46 -     1.58: 6177
        1.58 -     1.70: 0
        1.70 -     1.82: 133
  Bond restraints: 14256
  Sorted by residual:
  bond pdb=" N   ALA B 592 "
       pdb=" CA  ALA B 592 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.17e-02 7.31e+03 9.50e+00
  bond pdb=" N   ASP B 591 "
       pdb=" CA  ASP B 591 "
    ideal  model  delta    sigma   weight residual
    1.453  1.496 -0.043 1.41e-02 5.03e+03 9.37e+00
  bond pdb=" N   THR B 593 "
       pdb=" CA  THR B 593 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.19e-02 7.06e+03 7.82e+00
  bond pdb=" N   ASN B 594 "
       pdb=" CA  ASN B 594 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.39e-02 5.18e+03 5.83e+00
  bond pdb=" N   LEU A 315 "
       pdb=" CA  LEU A 315 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.50e+00
  ... (remaining 14251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 19124
        2.78 -     5.56: 164
        5.56 -     8.33: 16
        8.33 -    11.11: 2
       11.11 -    13.89: 2
  Bond angle restraints: 19308
  Sorted by residual:
  angle pdb=" C   PHE B 714 "
        pdb=" N   VAL B 715 "
        pdb=" CA  VAL B 715 "
      ideal   model   delta    sigma   weight residual
     122.13  129.84   -7.71 1.85e+00 2.92e-01 1.74e+01
  angle pdb=" CA  LEU A  37 "
        pdb=" CB  LEU A  37 "
        pdb=" CG  LEU A  37 "
      ideal   model   delta    sigma   weight residual
     116.30  130.19  -13.89 3.50e+00 8.16e-02 1.57e+01
  angle pdb=" N   THR B 593 "
        pdb=" CA  THR B 593 "
        pdb=" C   THR B 593 "
      ideal   model   delta    sigma   weight residual
     107.88  113.33   -5.45 1.41e+00 5.03e-01 1.49e+01
  angle pdb=" CB  MET A  11 "
        pdb=" CG  MET A  11 "
        pdb=" SD  MET A  11 "
      ideal   model   delta    sigma   weight residual
     112.70  123.71  -11.01 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" N   SER B 481 "
        pdb=" CA  SER B 481 "
        pdb=" C   SER B 481 "
      ideal   model   delta    sigma   weight residual
     108.23  113.07   -4.84 1.38e+00 5.25e-01 1.23e+01
  ... (remaining 19303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.04: 7529
       18.04 -    36.08: 856
       36.08 -    54.13: 213
       54.13 -    72.17: 37
       72.17 -    90.21: 15
  Dihedral angle restraints: 8650
    sinusoidal: 3620
      harmonic: 5030
  Sorted by residual:
  dihedral pdb=" CB  CYS B 241 "
           pdb=" SG  CYS B 241 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.79  -90.21     1      1.00e+01 1.00e-02 9.64e+01
  dihedral pdb=" CB  CYS B 288 "
           pdb=" SG  CYS B 288 "
           pdb=" SG  CYS B 301 "
           pdb=" CB  CYS B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.30  -88.70     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CB  CYS B 126 "
           pdb=" SG  CYS B 126 "
           pdb=" SG  CYS B 155 "
           pdb=" CB  CYS B 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    2.43  -88.43     1      1.00e+01 1.00e-02 9.34e+01
  ... (remaining 8647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1503
       0.042 -    0.084: 409
       0.084 -    0.126: 166
       0.126 -    0.168: 20
       0.168 -    0.210: 3
  Chirality restraints: 2101
  Sorted by residual:
  chirality pdb=" CB  VAL E  43 "
            pdb=" CA  VAL E  43 "
            pdb=" CG1 VAL E  43 "
            pdb=" CG2 VAL E  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CG  LEU B 411 "
            pdb=" CB  LEU B 411 "
            pdb=" CD1 LEU B 411 "
            pdb=" CD2 LEU B 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.30e-01
  chirality pdb=" CA  ILE B 781 "
            pdb=" N   ILE B 781 "
            pdb=" C   ILE B 781 "
            pdb=" CB  ILE B 781 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.92e-01
  ... (remaining 2098 not shown)

  Planarity restraints: 2491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 590 "    0.015 2.00e-02 2.50e+03   2.89e-02 8.33e+00
        pdb=" C   THR B 590 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   THR B 590 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP B 591 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 834 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO B 835 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 835 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 835 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 302 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO A 303 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 303 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 303 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2488 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 529
        2.71 -     3.25: 14129
        3.25 -     3.80: 23114
        3.80 -     4.35: 28910
        4.35 -     4.90: 46873
  Nonbonded interactions: 113555
  Sorted by model distance:
  nonbonded pdb=" NE  ARG D  40 "
            pdb=" OE2 GLU D  45 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" O   TYR B  67 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   SER B 878 "
            pdb=" OH  TYR B 882 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR B 127 "
            pdb=" O   ILE B 158 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   PHE B 714 "
            pdb=" NH1 ARG B 717 "
     model   vdw
     2.237 3.120
  ... (remaining 113550 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 518 or resid 528 through 539 or resid 546 throug \ 
h 656 or resid 701 through 905))
  selection = (chain 'B' and (resid 3 through 152 or resid 179 through 270 or resid 274 throug \ 
h 346 or resid 351 through 573 or resid 577 through 905))
}
ncs_group {
  reference = (chain 'C' and (resid 8 through 25 or resid 43 through 62))
  selection = (chain 'E' and (resid 8 through 41 or resid 43 through 62))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.980
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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      :  0.003   0.043  14256  Z= 0.190
  Angle     :  0.648  13.889  19308  Z= 0.339
  Chirality :  0.045   0.210   2101
  Planarity :  0.004   0.038   2491
  Dihedral  : 15.458  86.205   5277
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.19 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 18.48 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.21), residues: 1684
  helix: -0.90 (0.38), residues: 195
  sheet: -0.37 (0.29), residues: 348
  loop : -1.22 (0.19), residues: 1141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 412 
 HIS   0.008   0.001   HIS B 710 
 PHE   0.019   0.001   PHE D  48 
 TYR   0.011   0.001   TYR A 292 
 ARG   0.005   0.000   ARG D  38 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8300 (pp20)
REVERT: A  831 MET cc_start: 0.8281 (tpt) cc_final: 0.8004 (tpt)
  outliers start: 8
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2474
  time to fit residues: 27.8081
Evaluate side-chains
  62 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    3.9990
   chunk 129 optimal weight:    8.9990
   chunk 71 optimal weight:    8.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 69 optimal weight:   20.0000
   chunk 134 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 155 optimal weight:   30.0000
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 148 ASN
A 276 GLN
A 337 ASN
A 691 GLN
A 865 HIS
B 328 GLN
** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 ASN
B 594 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.096228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.064848 restraints weight = 55053.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.063012 restraints weight = 39199.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.063526 restraints weight = 30687.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14256  Z= 0.351
  Angle     :  0.645  10.909  19308  Z= 0.331
  Chirality :  0.046   0.203   2101
  Planarity :  0.004   0.042   2491
  Dihedral  :  5.393  79.115   1896
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.85 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.94 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.21), residues: 1684
  helix: -0.71 (0.38), residues: 194
  sheet: -0.63 (0.28), residues: 361
  loop : -1.27 (0.19), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 632 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.030   0.002   PHE C  19 
 TYR   0.019   0.001   TYR A 512 
 ARG   0.008   0.000   ARG D  40 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 57
  time to evaluate  : 1.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4483 (tp)
REVERT: A  318 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7384 (mm-30)
REVERT: A  329 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8462 (pp20)
REVERT: A  831 MET cc_start: 0.7885 (tpt) cc_final: 0.6775 (tpt)
REVERT: B  111 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7229 (t0)
REVERT: B  314 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8925 (mp)
REVERT: B  404 ASP cc_start: 0.8176 (t0) cc_final: 0.7867 (t0)
REVERT: B  897 TRP cc_start: 0.9426 (m100) cc_final: 0.9077 (m100)
REVERT: C    8 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5865 (pp)
REVERT: C   57 GLU cc_start: 0.8812 (tp30) cc_final: 0.8598 (tp30)
  outliers start: 52
  outliers final: 18
  residues processed: 105
  average time/residue: 0.2478
  time to fit residues: 40.9573
Evaluate side-chains
  77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 53
  time to evaluate  : 1.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  781 ILE
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 162 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 141 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 164 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9980
   chunk 122 optimal weight:    5.9990
   chunk 16 optimal weight:   30.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 247 HIS
A 691 GLN
A 764 ASN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 ASN
B 431 ASN
E  18 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.097674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.066095 restraints weight = 55014.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.065780 restraints weight = 35933.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.065324 restraints weight = 29951.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14256  Z= 0.168
  Angle     :  0.590   9.455  19308  Z= 0.301
  Chirality :  0.045   0.302   2101
  Planarity :  0.004   0.040   2491
  Dihedral  :  5.172  75.926   1896
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.66 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.97 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.21), residues: 1684
  helix: -0.65 (0.39), residues: 188
  sheet: -0.48 (0.28), residues: 363
  loop : -1.29 (0.19), residues: 1133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 632 
 HIS   0.006   0.001   HIS B 710 
 PHE   0.017   0.001   PHE A 705 
 TYR   0.018   0.001   TYR B 708 
 ARG   0.005   0.000   ARG D  40 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 68
  time to evaluate  : 1.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8688 (mmm) cc_final: 0.7655 (mpp)
REVERT: A  329 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: A  831 MET cc_start: 0.7922 (tpt) cc_final: 0.6851 (tpt)
REVERT: B  404 ASP cc_start: 0.8130 (t0) cc_final: 0.7720 (t0)
REVERT: C    8 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5720 (pp)
REVERT: D   40 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7917 (mmm-85)
  outliers start: 43
  outliers final: 18
  residues processed: 106
  average time/residue: 0.2415
  time to fit residues: 40.4827
Evaluate side-chains
  80 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 1.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 131 optimal weight:    6.9990
   chunk 170 optimal weight:    4.9990
   chunk 73 optimal weight:   30.0000
   chunk 152 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 138 optimal weight:    6.9990
   chunk 154 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
A 610 GLN
A 691 GLN
B  90 ASN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.096286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.062842 restraints weight = 54709.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063556 restraints weight = 36456.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063673 restraints weight = 25502.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14256  Z= 0.303
  Angle     :  0.617   8.908  19308  Z= 0.316
  Chirality :  0.046   0.288   2101
  Planarity :  0.004   0.040   2491
  Dihedral  :  4.803  50.945   1893
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.55 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 17.97 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.21), residues: 1684
  helix: -0.74 (0.38), residues: 194
  sheet: -0.55 (0.28), residues: 363
  loop : -1.32 (0.19), residues: 1127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 632 
 HIS   0.006   0.001   HIS B 710 
 PHE   0.023   0.001   PHE C  19 
 TYR   0.016   0.001   TYR A 512 
 ARG   0.006   0.000   ARG D  49 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 58
  time to evaluate  : 1.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8676 (mmm) cc_final: 0.7753 (mpp)
REVERT: A  110 MET cc_start: 0.7528 (mmm) cc_final: 0.7255 (mmm)
REVERT: A  314 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4124 (tp)
REVERT: B  111 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7263 (t0)
REVERT: B  314 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9006 (mp)
REVERT: B  404 ASP cc_start: 0.8347 (t0) cc_final: 0.7970 (t0)
REVERT: B  582 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9209 (ptmm)
REVERT: B  831 MET cc_start: 0.6698 (mmm) cc_final: 0.6316 (tpt)
REVERT: C    8 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5537 (pp)
  outliers start: 58
  outliers final: 31
  residues processed: 113
  average time/residue: 0.2129
  time to fit residues: 39.5483
Evaluate side-chains
  90 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 54
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 146 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 136 optimal weight:   10.0000
   chunk 5 optimal weight:   50.0000
   chunk 8 optimal weight:    9.9990
   chunk 121 optimal weight:    3.9990
   chunk 71 optimal weight:   50.0000
   chunk 19 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
A 337 ASN
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 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 = 0.4087 r_free = 0.4087 target = 0.095824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.064769 restraints weight = 55100.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.062882 restraints weight = 34395.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.063075 restraints weight = 29754.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  14256  Z= 0.338
  Angle     :  0.635  10.105  19308  Z= 0.324
  Chirality :  0.046   0.246   2101
  Planarity :  0.004   0.041   2491
  Dihedral  :  4.889  47.806   1893
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.55 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.61 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.20), residues: 1684
  helix: -0.71 (0.38), residues: 188
  sheet: -0.58 (0.28), residues: 361
  loop : -1.37 (0.19), residues: 1135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 412 
 HIS   0.006   0.001   HIS B 710 
 PHE   0.021   0.001   PHE C  19 
 TYR   0.021   0.001   TYR B 708 
 ARG   0.004   0.000   ARG D  40 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 54
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8622 (mmm) cc_final: 0.7725 (mpp)
REVERT: A  314 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4246 (tp)
REVERT: A  318 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7344 (mm-30)
REVERT: B  111 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (t0)
REVERT: B  314 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9059 (mp)
REVERT: B  404 ASP cc_start: 0.8101 (t0) cc_final: 0.7677 (t0)
REVERT: B  831 MET cc_start: 0.6848 (mmm) cc_final: 0.6385 (tpt)
REVERT: C    8 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5675 (pp)
  outliers start: 60
  outliers final: 41
  residues processed: 111
  average time/residue: 0.2243
  time to fit residues: 39.3343
Evaluate side-chains
  98 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 52
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  159 CYS
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  260 GLN
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  769 VAL
Chi-restraints excluded: chain B residue  781 ILE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 96 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 8 optimal weight:   30.0000
   chunk 157 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 337 ASN
A 513 GLN
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.094738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.063091 restraints weight = 55718.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061898 restraints weight = 38817.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.061683 restraints weight = 31808.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  14256  Z= 0.458
  Angle     :  0.705  10.737  19308  Z= 0.358
  Chirality :  0.047   0.235   2101
  Planarity :  0.004   0.041   2491
  Dihedral  :  5.163  45.539   1893
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.56 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 18.61 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.20), residues: 1684
  helix: -1.08 (0.37), residues: 196
  sheet: -0.71 (0.28), residues: 361
  loop : -1.47 (0.18), residues: 1127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 412 
 HIS   0.007   0.001   HIS B 548 
 PHE   0.024   0.002   PHE C  19 
 TYR   0.025   0.002   TYR A 512 
 ARG   0.005   0.001   ARG D  40 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 52
  time to evaluate  : 1.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: A  314 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4495 (tp)
REVERT: A  477 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8130 (p90)
REVERT: B  314 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9117 (mp)
REVERT: B  404 ASP cc_start: 0.7919 (t0) cc_final: 0.7486 (t0)
REVERT: B  831 MET cc_start: 0.7099 (mmm) cc_final: 0.6589 (tpt)
REVERT: C    8 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6184 (pp)
  outliers start: 72
  outliers final: 42
  residues processed: 123
  average time/residue: 0.2012
  time to fit residues: 40.7525
Evaluate side-chains
  96 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 49
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  691 GLN
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  159 CYS
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  260 GLN
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  769 VAL
Chi-restraints excluded: chain B residue  781 ILE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 93 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 136 optimal weight:    7.9990
   chunk 162 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 ASN
** B 264 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 = 0.4086 r_free = 0.4086 target = 0.096021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.061184 restraints weight = 54757.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.062945 restraints weight = 34558.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063220 restraints weight = 23299.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14256  Z= 0.227
  Angle     :  0.630  12.121  19308  Z= 0.319
  Chirality :  0.046   0.338   2101
  Planarity :  0.004   0.043   2491
  Dihedral  :  4.968  43.405   1893
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.66 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.76 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.20), residues: 1684
  helix: -0.85 (0.38), residues: 189
  sheet: -0.62 (0.28), residues: 358
  loop : -1.40 (0.19), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 412 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.017   0.001   PHE A 705 
 TYR   0.013   0.001   TYR A 512 
 ARG   0.005   0.000   ARG A 757 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 55
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8143 (mm)
REVERT: A  314 LEU cc_start: 0.4725 (OUTLIER) cc_final: 0.4184 (tp)
REVERT: A  318 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7124 (mm-30)
REVERT: A  477 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8219 (p90)
REVERT: B   59 ASP cc_start: 0.8716 (m-30) cc_final: 0.8306 (m-30)
REVERT: B  314 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9034 (mp)
REVERT: B  831 MET cc_start: 0.7006 (mmm) cc_final: 0.6525 (tpt)
REVERT: C    8 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6182 (pp)
  outliers start: 54
  outliers final: 35
  residues processed: 109
  average time/residue: 0.2157
  time to fit residues: 38.0945
Evaluate side-chains
  96 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 55
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  757 ARG
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  159 CYS
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 163 optimal weight:    0.3980
   chunk 146 optimal weight:    0.8980
   chunk 123 optimal weight:    7.9990
   chunk 69 optimal weight:   40.0000
   chunk 31 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0270
   chunk 50 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.0642

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.095810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.061681 restraints weight = 54807.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062822 restraints weight = 35911.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.063217 restraints weight = 25208.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14256  Z= 0.258
  Angle     :  0.639  12.161  19308  Z= 0.322
  Chirality :  0.046   0.322   2101
  Planarity :  0.004   0.042   2491
  Dihedral  :  4.805  42.910   1891
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.03 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.14 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.20), residues: 1684
  helix: -0.85 (0.38), residues: 188
  sheet: -0.59 (0.28), residues: 358
  loop : -1.40 (0.19), residues: 1138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 412 
 HIS   0.004   0.001   HIS B 710 
 PHE   0.017   0.001   PHE C  19 
 TYR   0.014   0.001   TYR A 512 
 ARG   0.005   0.000   ARG A 757 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 56
  time to evaluate  : 1.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8248 (mm)
REVERT: A  318 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7011 (mm-30)
REVERT: A  477 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8219 (p90)
REVERT: B   59 ASP cc_start: 0.8702 (m-30) cc_final: 0.8284 (m-30)
REVERT: B  314 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9058 (mp)
REVERT: B  404 ASP cc_start: 0.8415 (t0) cc_final: 0.8150 (t0)
REVERT: B  831 MET cc_start: 0.7125 (mmm) cc_final: 0.6736 (tpt)
REVERT: E   12 GLU cc_start: 0.8654 (pm20) cc_final: 0.8197 (pm20)
  outliers start: 48
  outliers final: 36
  residues processed: 104
  average time/residue: 0.2118
  time to fit residues: 36.5887
Evaluate side-chains
  95 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 55
  time to evaluate  : 1.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  691 GLN
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  159 CYS
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 121 optimal weight:    0.9980
   chunk 165 optimal weight:    0.3980
   chunk 106 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:   50.0000
   chunk 132 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.096593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.062440 restraints weight = 54391.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.064076 restraints weight = 35170.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.064290 restraints weight = 21957.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14256  Z= 0.172
  Angle     :  0.629  12.535  19308  Z= 0.315
  Chirality :  0.046   0.315   2101
  Planarity :  0.004   0.043   2491
  Dihedral  :  4.681  41.891   1891
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.60 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.78 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.21), residues: 1684
  helix: -0.89 (0.37), residues: 200
  sheet: -0.44 (0.29), residues: 351
  loop : -1.40 (0.19), residues: 1133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B 440 
 PHE   0.019   0.001   PHE A 705 
 TYR   0.010   0.001   TYR B 628 
 ARG   0.005   0.000   ARG A 757 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 59
  time to evaluate  : 1.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: A  318 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7078 (mm-30)
REVERT: A  477 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8192 (p90)
REVERT: B   59 ASP cc_start: 0.8564 (m-30) cc_final: 0.8171 (m-30)
REVERT: B  314 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8992 (mp)
REVERT: B  404 ASP cc_start: 0.8090 (t0) cc_final: 0.7864 (t0)
REVERT: B  831 MET cc_start: 0.7088 (mmm) cc_final: 0.6681 (tpt)
REVERT: E   12 GLU cc_start: 0.8633 (pm20) cc_final: 0.8191 (pm20)
  outliers start: 38
  outliers final: 30
  residues processed: 97
  average time/residue: 0.2143
  time to fit residues: 33.7659
Evaluate side-chains
  91 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 57
  time to evaluate  : 1.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  691 GLN
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  805 THR
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   62 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 144 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 128 optimal weight:    0.6980
   chunk 160 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 5 optimal weight:   10.0000
   chunk 151 optimal weight:   30.0000
   chunk 118 optimal weight:    0.9980
   chunk 138 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.096513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.062178 restraints weight = 54949.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.064105 restraints weight = 35704.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.064044 restraints weight = 21931.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14256  Z= 0.192
  Angle     :  0.626  12.691  19308  Z= 0.313
  Chirality :  0.045   0.306   2101
  Planarity :  0.003   0.043   2491
  Dihedral  :  4.638  41.648   1891
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.90 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.91 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.21), residues: 1684
  helix: -0.87 (0.37), residues: 201
  sheet: -0.43 (0.28), residues: 356
  loop : -1.36 (0.19), residues: 1127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B 440 
 PHE   0.017   0.001   PHE A 705 
 TYR   0.011   0.001   TYR B 628 
 ARG   0.005   0.000   ARG D  40 

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 56
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8172 (mm)
REVERT: A  318 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7039 (mm-30)
REVERT: A  477 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8174 (p90)
REVERT: A  806 MET cc_start: 0.8411 (ptp) cc_final: 0.8154 (pmm)
REVERT: A  831 MET cc_start: 0.8279 (tpt) cc_final: 0.7398 (tpt)
REVERT: B   59 ASP cc_start: 0.8566 (m-30) cc_final: 0.8183 (m-30)
REVERT: B  314 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (mp)
REVERT: B  404 ASP cc_start: 0.8031 (t0) cc_final: 0.7798 (t0)
REVERT: B  831 MET cc_start: 0.7002 (mmm) cc_final: 0.6627 (tpt)
REVERT: E   12 GLU cc_start: 0.8664 (pm20) cc_final: 0.8230 (pm20)
  outliers start: 38
  outliers final: 30
  residues processed: 94
  average time/residue: 0.2333
  time to fit residues: 35.5345
Evaluate side-chains
  89 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 55
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  479 ARG
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  805 THR
Chi-restraints excluded: chain C residue   47 CYS
Chi-restraints excluded: chain D residue   42 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 63 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 136 optimal weight:    8.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 691 GLN
** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 ASN
** B 264 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 = 0.4090 r_free = 0.4090 target = 0.096137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061884 restraints weight = 55031.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063055 restraints weight = 38070.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.063322 restraints weight = 25354.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14256  Z= 0.224
  Angle     :  0.629  12.496  19308  Z= 0.313
  Chirality :  0.045   0.291   2101
  Planarity :  0.004   0.042   2491
  Dihedral  :  4.631  41.641   1891
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.14 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.78 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.21), residues: 1684
  helix: -0.89 (0.37), residues: 202
  sheet: -0.46 (0.29), residues: 351
  loop : -1.36 (0.19), residues: 1131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B 440 
 PHE   0.015   0.001   PHE C  19 
 TYR   0.012   0.001   TYR B 628 
 ARG   0.004   0.000   ARG A 757 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4081.18 seconds
wall clock time: 74 minutes 18.02 seconds (4458.02 seconds total)