Starting phenix.real_space_refine
on Wed Mar  4 22:19:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sth_25428/03_2026/7sth_25428_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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 3460 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     112      5.16       5
     C    8898      2.51       5
     N    2402      2.21       5
     O    2598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14010
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 820, 6629
          Classifications: {'peptide': 820}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 6629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 820, 6629
          Classifications: {'peptide': 820}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 376
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 376
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
          Chain breaks: 1
  Time building chain proxies: 3.26, per 1000 atoms: 0.23
  Number of scatterers: 14010
  At special positions: 0
  Unit cell: (139.32, 113.4, 174.96, 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     112     16.00
     O    2598      8.00
     N    2402      7.00
     C    8898      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=40, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " 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=2.04
    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 861 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 787 " - pdb=" SG  CYS A 796 " 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=2.03
    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 861 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 787 " - pdb=" SG  CYS B 796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS C  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  66 " 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: 1.01
  Conformation dependent library (CDL) restraints added in 551.4 milliseconds
  

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3276

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 33 sheets defined
      16.5% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 23
      removed outlier: 4.080A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU A  22 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A  23 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 18 through 23'
    Processing helix  chain 'A' and resid 43 through 48
      removed outlier: 3.939A  pdb=" N   ARG A  47 " --> pdb=" O   PRO A  43 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ASP A  48 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 43 through 48'
    Processing helix  chain 'A' and resid 132 through 136
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 221 through 225
      removed outlier: 3.737A  pdb=" N   CYS A 225 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.575A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.653A  pdb=" N   GLU A 318 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 329 through 331
      No H-bonds generated for 'chain 'A' and resid 329 through 331'
    Processing helix  chain 'A' and resid 350 through 358
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.544A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 3.900A  pdb=" N   PHE A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 715
    Processing helix  chain 'A' and resid 864 through 871
    Processing helix  chain 'B' and resid 19 through 23
      removed outlier: 3.916A  pdb=" N   GLU B  22 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B  23 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 19 through 23'
    Processing helix  chain 'B' and resid 43 through 48
      removed outlier: 3.991A  pdb=" N   ARG B  47 " --> pdb=" O   PRO B  43 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ASP B  48 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 43 through 48'
    Processing helix  chain 'B' and resid 132 through 136
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'B' and resid 221 through 225
      removed outlier: 3.712A  pdb=" N   CYS B 225 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 268
      removed outlier: 3.569A  pdb=" N   CYS B 259 " --> pdb=" O   ASN B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 318
      removed outlier: 3.600A  pdb=" N   GLU B 318 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
    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 447
      removed outlier: 3.661A  pdb=" N   GLY B 447 " --> pdb=" O   GLU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 638 through 644
      removed outlier: 3.682A  pdb=" N   LEU B 644 " --> pdb=" O   LEU B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 715
    Processing helix  chain 'B' and resid 864 through 871
    Processing helix  chain 'C' and resid 8 through 19
      removed outlier: 3.776A  pdb=" N   VAL C  12 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 62
    Processing helix  chain 'C' and resid 67 through 72
      removed outlier: 3.610A  pdb=" N   LEU C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU C  72 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 67 through 72'
    Processing helix  chain 'D' and resid 8 through 19
      removed outlier: 3.773A  pdb=" N   VAL D  12 " --> pdb=" O   GLY D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 62
    Processing helix  chain 'D' and resid 68 through 72
      removed outlier: 4.104A  pdb=" N   GLU D  72 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
      removed outlier: 3.522A  pdb=" N   LEU A  36 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ARG A 118 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL A  94 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   GLU A 120 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   PHE A  96 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ASN A 122 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL A 117 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   VAL A 146 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE A 119 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ASN A 148 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LYS A 121 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
      removed outlier: 3.689A  pdb=" N   VAL A 179 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184
      removed outlier: 6.625A  pdb=" N   HIS A 187 " --> pdb=" O   TRP A 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254
      removed outlier: 6.920A  pdb=" N   HIS A 247 " --> pdb=" O   CYS A 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321
      removed outlier: 6.866A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   HIS A 429 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ALA A 402 " --> pdb=" O   HIS A 429 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473
    Processing sheet with id=AB2, first strand: chain 'A' and resid 479 through 480
    Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534
      removed outlier: 3.560A  pdb=" N   GLY A 502 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 599 through 607
      removed outlier: 5.931A  pdb=" N   ASP A 600 " --> pdb=" O   LYS A 616 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LYS A 616 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   GLN A 610 " --> pdb=" O   ASN A 606 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 634 through 635
      removed outlier: 3.762A  pdb=" N   GLY A 779 " --> pdb=" O   GLN A 635 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 630 " --> pdb=" O   GLU A 761 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 634 through 635
      removed outlier: 3.762A  pdb=" N   GLY A 779 " --> pdb=" O   GLN A 635 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 820 through 823
    Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 863
      removed outlier: 6.850A  pdb=" N   THR A 890 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR A 846 " --> pdb=" O   ARG A 888 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ARG A 888 " --> pdb=" O   TYR A 846 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   VAL A 848 " --> pdb=" O   ARG A 886 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ARG A 886 " --> pdb=" O   VAL A 848 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   TYR A 850 " --> pdb=" O   SER A 884 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   SER A 884 " --> pdb=" O   TYR A 850 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG A 852 " --> pdb=" O   ASN A 882 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ASN A 882 " --> pdb=" O   ARG A 852 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.739A  pdb=" N   VAL B  66 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   ARG B 118 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   VAL B  94 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   GLU B 120 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   PHE B  96 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ASN B 122 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL B 117 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   VAL B 146 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE B 119 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ASN B 148 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   LYS B 121 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29
    Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.695A  pdb=" N   VAL B 179 " --> pdb=" O   THR B 172 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184
      removed outlier: 6.630A  pdb=" N   HIS B 187 " --> pdb=" O   TRP B 183 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232
      removed outlier: 3.633A  pdb=" N   PHE B 231 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.897A  pdb=" N   HIS B 247 " --> pdb=" O   CYS B 284 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294
    Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 312
    Processing sheet with id=AC8, first strand: chain 'B' and resid 319 through 321
      removed outlier: 6.865A  pdb=" N   LYS B 319 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   HIS B 429 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ALA B 402 " --> pdb=" O   HIS B 429 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473
    Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480
    Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534
      removed outlier: 3.592A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 599 through 604
      removed outlier: 5.570A  pdb=" N   ASP B 600 " --> pdb=" O   LYS B 616 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 616 " --> pdb=" O   ASP B 600 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 760 through 763
      removed outlier: 3.869A  pdb=" N   VAL B 630 " --> pdb=" O   GLU B 761 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 820 through 823
    Processing sheet with id=AD6, first strand: chain 'B' and resid 858 through 863
      removed outlier: 3.885A  pdb=" N   LEU B 845 " --> pdb=" O   THR B 890 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    873 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: 2.60

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4583
        1.34 -     1.46: 3384
        1.46 -     1.58: 6249
        1.58 -     1.70: 0
        1.70 -     1.82: 136
  Bond restraints: 14352
  Sorted by residual:
  bond pdb=" C   CYS A 686 "
       pdb=" N   PRO A 687 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.19e-02 7.06e+03 1.82e+00
  bond pdb=" CA  ASP B 690 "
       pdb=" C   ASP B 690 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.28e-02 6.10e+03 1.49e+00
  bond pdb=" CA  THR B 689 "
       pdb=" CB  THR B 689 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.017 1.41e-02 5.03e+03 1.39e+00
  bond pdb=" CA  VAL A 158 "
       pdb=" CB  VAL A 158 "
    ideal  model  delta    sigma   weight residual
    1.528  1.543 -0.015 1.34e-02 5.57e+03 1.21e+00
  bond pdb=" N   SER A 691 "
       pdb=" CA  SER A 691 "
    ideal  model  delta    sigma   weight residual
    1.459  1.447  0.013 1.20e-02 6.94e+03 1.10e+00
  ... (remaining 14347 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 18893
        1.42 -     2.85: 460
        2.85 -     4.27: 84
        4.27 -     5.69: 9
        5.69 -     7.12: 8
  Bond angle restraints: 19454
  Sorted by residual:
  angle pdb=" C   THR B 578 "
        pdb=" N   TYR B 579 "
        pdb=" CA  TYR B 579 "
      ideal   model   delta    sigma   weight residual
     121.54  128.66   -7.12 1.91e+00 2.74e-01 1.39e+01
  angle pdb=" C   THR A 578 "
        pdb=" N   TYR A 579 "
        pdb=" CA  TYR A 579 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" CA  GLY A 502 "
        pdb=" C   GLY A 502 "
        pdb=" N   PHE A 503 "
      ideal   model   delta    sigma   weight residual
     114.23  116.91   -2.68 8.80e-01 1.29e+00 9.27e+00
  angle pdb=" OG1 THR B 689 "
        pdb=" CB  THR B 689 "
        pdb=" CG2 THR B 689 "
      ideal   model   delta    sigma   weight residual
     109.30  103.33    5.97 2.00e+00 2.50e-01 8.90e+00
  angle pdb=" OG1 THR A 689 "
        pdb=" CB  THR A 689 "
        pdb=" CG2 THR A 689 "
      ideal   model   delta    sigma   weight residual
     109.30  103.36    5.94 2.00e+00 2.50e-01 8.83e+00
  ... (remaining 19449 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 7785
       17.24 -    34.49: 733
       34.49 -    51.73: 142
       51.73 -    68.97: 32
       68.97 -    86.21: 14
  Dihedral angle restraints: 8706
    sinusoidal: 3634
      harmonic: 5072
  Sorted by residual:
  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 -143.08   57.08     1      1.00e+01 1.00e-02 4.38e+01
  dihedral pdb=" CB  CYS A 126 "
           pdb=" SG  CYS A 126 "
           pdb=" SG  CYS A 155 "
           pdb=" CB  CYS A 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.34   56.34     1      1.00e+01 1.00e-02 4.28e+01
  dihedral pdb=" CB  CYS B 266 "
           pdb=" SG  CYS B 266 "
           pdb=" SG  CYS B 274 "
           pdb=" CB  CYS B 274 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.72  -54.72     1      1.00e+01 1.00e-02 4.06e+01
  ... (remaining 8703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1351
       0.033 -    0.067: 490
       0.067 -    0.100: 163
       0.100 -    0.133: 105
       0.133 -    0.166: 3
  Chirality restraints: 2112
  Sorted by residual:
  chirality pdb=" CB  THR A 689 "
            pdb=" CA  THR A 689 "
            pdb=" OG1 THR A 689 "
            pdb=" CG2 THR A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CB  THR B 689 "
            pdb=" CA  THR B 689 "
            pdb=" OG1 THR B 689 "
            pdb=" CG2 THR B 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CA  ILE A 564 "
            pdb=" N   ILE A 564 "
            pdb=" C   ILE A 564 "
            pdb=" CB  ILE A 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 2109 not shown)

  Planarity restraints: 2514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 578 "   -0.012 2.00e-02 2.50e+03   2.52e-02 6.35e+00
        pdb=" C   THR B 578 "    0.044 2.00e-02 2.50e+03
        pdb=" O   THR B 578 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR B 579 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 578 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   THR A 578 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR A 578 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A 579 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 835 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO A 836 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 836 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 836 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2511 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1097
        2.74 -     3.28: 14060
        3.28 -     3.82: 22516
        3.82 -     4.36: 26993
        4.36 -     4.90: 45996
  Nonbonded interactions: 110662
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 499 "
            pdb=" OH  TYR A 579 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OE2 GLU A 699 "
            pdb=" OH  TYR B 144 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PRO B  77 "
            pdb=" ND2 ASN B 108 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OH  TYR A 144 "
            pdb=" OE2 GLU B 699 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLU A 825 "
            pdb=" OH  TYR A 909 "
     model   vdw
     2.236 3.040
  ... (remaining 110657 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.720
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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   0.034  14392  Z= 0.134
  Angle     :  0.558   7.117  19534  Z= 0.299
  Chirality :  0.044   0.166   2112
  Planarity :  0.003   0.036   2514
  Dihedral  : 13.675  86.213   5310
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.47 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.44 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.21), residues: 1700
  helix: -0.30 (0.36), residues: 222
  sheet: -0.21 (0.29), residues: 348
  loop : -1.26 (0.19), residues: 1130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 554 
 TYR   0.020   0.001   TYR B 579 
 PHE   0.018   0.001   PHE B 706 
 TRP   0.018   0.001   TRP B 412 
 HIS   0.004   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (14352)
  covalent geometry    : angle       0.55593 (19454)
  SS BOND              : bond        0.00245 (   40)
  SS BOND              : angle       0.95910 (   80)
  hydrogen bonds       : bond        0.23244 (  329)
  hydrogen bonds       : angle       8.57083 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.5889 (m-10) cc_final: 0.5641 (m-80)
REVERT: B  646 TYR cc_start: 0.5846 (m-10) cc_final: 0.5284 (m-80)
REVERT: B  807 MET cc_start: 0.8326 (mmp) cc_final: 0.8009 (mmm)
REVERT: B  845 LEU cc_start: 0.9207 (pt) cc_final: 0.9001 (pp)
  outliers start: 6
  outliers final: 2
  residues processed: 77
  average time/residue: 0.0968
  time to fit residues: 11.8945
Evaluate side-chains
  60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain B residue  686 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 470 ASN
B 692 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.112967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.074438 restraints weight = 34630.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.074841 restraints weight = 22489.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.076535 restraints weight = 15204.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.076658 restraints weight = 13910.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.076607 restraints weight = 12477.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14392  Z= 0.154
  Angle     :  0.586   9.123  19534  Z= 0.306
  Chirality :  0.045   0.185   2112
  Planarity :  0.004   0.035   2514
  Dihedral  :  4.677  42.989   1896
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.82 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.82 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.21), residues: 1700
  helix: -0.19 (0.36), residues: 226
  sheet: -0.06 (0.30), residues: 352
  loop : -1.20 (0.20), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 554 
 TYR   0.017   0.001   TYR B 507 
 PHE   0.017   0.001   PHE B 706 
 TRP   0.015   0.001   TRP A 833 
 HIS   0.007   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (14352)
  covalent geometry    : angle       0.58490 (19454)
  SS BOND              : bond        0.00294 (   40)
  SS BOND              : angle       0.81498 (   80)
  hydrogen bonds       : bond        0.05230 (  329)
  hydrogen bonds       : angle       6.53109 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6081 (m-10) cc_final: 0.5777 (m-80)
REVERT: B  646 TYR cc_start: 0.5958 (m-10) cc_final: 0.5553 (m-80)
REVERT: B  898 TRP cc_start: 0.7756 (m100) cc_final: 0.7474 (m100)
  outliers start: 8
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0854
  time to fit residues: 9.9020
Evaluate side-chains
  59 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain B residue  905 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 163 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 156 optimal weight:   30.0000
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 470 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.110745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.073498 restraints weight = 35167.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.073748 restraints weight = 19745.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.073623 restraints weight = 15738.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.074057 restraints weight = 14900.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.074140 restraints weight = 14498.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  14392  Z= 0.263
  Angle     :  0.624   7.881  19534  Z= 0.323
  Chirality :  0.046   0.208   2112
  Planarity :  0.004   0.044   2514
  Dihedral  :  4.931  43.901   1895
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.47 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.30 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.21), residues: 1700
  helix: -0.35 (0.35), residues: 236
  sheet: -0.08 (0.30), residues: 340
  loop : -1.24 (0.20), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 345 
 TYR   0.019   0.002   TYR B 507 
 PHE   0.018   0.002   PHE B 565 
 TRP   0.028   0.002   TRP A 833 
 HIS   0.007   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (14352)
  covalent geometry    : angle       0.62287 (19454)
  SS BOND              : bond        0.00402 (   40)
  SS BOND              : angle       0.89842 (   80)
  hydrogen bonds       : bond        0.05137 (  329)
  hydrogen bonds       : angle       6.21312 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6351 (m-10) cc_final: 0.5914 (m-80)
REVERT: A  898 TRP cc_start: 0.7542 (m100) cc_final: 0.7147 (m100)
REVERT: B  646 TYR cc_start: 0.6180 (m-10) cc_final: 0.5780 (m-80)
REVERT: B  898 TRP cc_start: 0.7588 (m100) cc_final: 0.7135 (m100)
REVERT: D   70 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7984 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 68
  average time/residue: 0.0854
  time to fit residues: 9.9932
Evaluate side-chains
  64 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain D residue   70 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0020
   chunk 77 optimal weight:   20.0000
   chunk 166 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0970
   chunk 147 optimal weight:    0.5980
   chunk 163 optimal weight:   20.0000
   chunk 1 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  70 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.113279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.076573 restraints weight = 34873.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.076884 restraints weight = 19459.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.077032 restraints weight = 15022.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.077487 restraints weight = 14467.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.077604 restraints weight = 13294.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  14392  Z= 0.101
  Angle     :  0.535   9.087  19534  Z= 0.278
  Chirality :  0.043   0.191   2112
  Planarity :  0.003   0.034   2514
  Dihedral  :  4.596  45.325   1895
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.00 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.82 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.22), residues: 1700
  helix: -0.16 (0.37), residues: 226
  sheet:  0.21 (0.31), residues: 328
  loop : -1.14 (0.20), residues: 1146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 345 
 TYR   0.014   0.001   TYR A 579 
 PHE   0.021   0.001   PHE B 706 
 TRP   0.025   0.001   TRP A 833 
 HIS   0.004   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (14352)
  covalent geometry    : angle       0.53405 (19454)
  SS BOND              : bond        0.00233 (   40)
  SS BOND              : angle       0.65479 (   80)
  hydrogen bonds       : bond        0.04117 (  329)
  hydrogen bonds       : angle       5.76754 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6262 (m-10) cc_final: 0.5824 (m-80)
REVERT: A  898 TRP cc_start: 0.7564 (m100) cc_final: 0.7171 (m100)
REVERT: B  646 TYR cc_start: 0.6172 (m-10) cc_final: 0.5794 (m-80)
REVERT: B  898 TRP cc_start: 0.7501 (m100) cc_final: 0.7217 (m100)
REVERT: C   70 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7992 (pm20)
  outliers start: 15
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0834
  time to fit residues: 11.1958
Evaluate side-chains
  69 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   70 GLN
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 159 optimal weight:    9.9990
   chunk 137 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 148 optimal weight:    2.9990
   chunk 157 optimal weight:    8.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.110016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.072159 restraints weight = 35317.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.072194 restraints weight = 21569.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.072634 restraints weight = 16289.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.072993 restraints weight = 16095.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.073178 restraints weight = 14412.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  14392  Z= 0.298
  Angle     :  0.642   9.299  19534  Z= 0.328
  Chirality :  0.046   0.212   2112
  Planarity :  0.004   0.035   2514
  Dihedral  :  4.898  45.218   1895
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.88 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.34 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.21), residues: 1700
  helix: -0.33 (0.36), residues: 236
  sheet: -0.03 (0.30), residues: 340
  loop : -1.23 (0.20), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  14 
 TYR   0.020   0.002   TYR B 507 
 PHE   0.020   0.002   PHE B 565 
 TRP   0.028   0.002   TRP A 833 
 HIS   0.004   0.001   HIS B 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 (14352)
  covalent geometry    : angle       0.64043 (19454)
  SS BOND              : bond        0.00427 (   40)
  SS BOND              : angle       0.92752 (   80)
  hydrogen bonds       : bond        0.04744 (  329)
  hydrogen bonds       : angle       5.85084 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6446 (m-10) cc_final: 0.5910 (m-80)
REVERT: A  898 TRP cc_start: 0.7910 (m100) cc_final: 0.7414 (m100)
REVERT: B   98 MET cc_start: 0.8634 (tpt) cc_final: 0.8111 (tpt)
REVERT: B  110 MET cc_start: 0.8204 (ptp) cc_final: 0.7992 (ptp)
REVERT: B  442 MET cc_start: 0.9314 (mmm) cc_final: 0.8768 (tpp)
REVERT: B  646 TYR cc_start: 0.6170 (m-10) cc_final: 0.5639 (m-80)
REVERT: B  807 MET cc_start: 0.8048 (mmm) cc_final: 0.7689 (mmm)
REVERT: B  898 TRP cc_start: 0.7907 (m100) cc_final: 0.7591 (m100)
  outliers start: 20
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0822
  time to fit residues: 10.6250
Evaluate side-chains
  67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 164 optimal weight:   10.0000
   chunk 140 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 112 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
B  90 ASN
B 111 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 440 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.111891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.074466 restraints weight = 35002.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.074872 restraints weight = 20787.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.075027 restraints weight = 15104.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075463 restraints weight = 15154.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075543 restraints weight = 13893.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14392  Z= 0.118
  Angle     :  0.545   9.384  19534  Z= 0.282
  Chirality :  0.043   0.197   2112
  Planarity :  0.003   0.035   2514
  Dihedral  :  4.660  45.752   1895
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.94 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.03 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.22), residues: 1700
  helix: -0.23 (0.36), residues: 236
  sheet:  0.17 (0.31), residues: 328
  loop : -1.14 (0.20), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 345 
 TYR   0.015   0.001   TYR B 507 
 PHE   0.020   0.001   PHE B 706 
 TRP   0.026   0.001   TRP A 833 
 HIS   0.004   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (14352)
  covalent geometry    : angle       0.54460 (19454)
  SS BOND              : bond        0.00259 (   40)
  SS BOND              : angle       0.66302 (   80)
  hydrogen bonds       : bond        0.04093 (  329)
  hydrogen bonds       : angle       5.58864 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6369 (m-10) cc_final: 0.5971 (m-80)
REVERT: A  898 TRP cc_start: 0.7669 (m100) cc_final: 0.7273 (m100)
REVERT: B   98 MET cc_start: 0.8632 (tpt) cc_final: 0.8408 (tpt)
REVERT: B  646 TYR cc_start: 0.6233 (m-10) cc_final: 0.5754 (m-80)
REVERT: B  898 TRP cc_start: 0.7589 (m100) cc_final: 0.7348 (m100)
  outliers start: 22
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0805
  time to fit residues: 11.3387
Evaluate side-chains
  71 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   68 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 123 optimal weight:    0.1980
   chunk 15 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 126 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.112928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.076135 restraints weight = 34813.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076335 restraints weight = 20400.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.076260 restraints weight = 15534.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.076796 restraints weight = 14962.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.077010 restraints weight = 13813.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14392  Z= 0.104
  Angle     :  0.530  10.129  19534  Z= 0.275
  Chirality :  0.043   0.205   2112
  Planarity :  0.003   0.035   2514
  Dihedral  :  4.491  47.137   1895
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.65 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.48 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.22), residues: 1700
  helix: -0.12 (0.37), residues: 226
  sheet:  0.26 (0.31), residues: 328
  loop : -1.08 (0.20), residues: 1146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 554 
 TYR   0.013   0.001   TYR A 507 
 PHE   0.020   0.001   PHE B 706 
 TRP   0.032   0.001   TRP A 833 
 HIS   0.004   0.001   HIS B 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (14352)
  covalent geometry    : angle       0.53024 (19454)
  SS BOND              : bond        0.00229 (   40)
  SS BOND              : angle       0.57730 (   80)
  hydrogen bonds       : bond        0.03730 (  329)
  hydrogen bonds       : angle       5.33312 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A  300 MET cc_start: 0.8776 (mpp) cc_final: 0.8269 (tpt)
REVERT: A  646 TYR cc_start: 0.6364 (m-10) cc_final: 0.5943 (m-80)
REVERT: A  898 TRP cc_start: 0.7586 (m100) cc_final: 0.7243 (m100)
REVERT: B  300 MET cc_start: 0.8758 (mpp) cc_final: 0.8464 (tpt)
REVERT: B  646 TYR cc_start: 0.6129 (m-10) cc_final: 0.5649 (m-80)
REVERT: B  807 MET cc_start: 0.7974 (mmm) cc_final: 0.7723 (mmm)
  outliers start: 18
  outliers final: 14
  residues processed: 78
  average time/residue: 0.0860
  time to fit residues: 11.4510
Evaluate side-chains
  76 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain D residue   70 GLN
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.111087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.072854 restraints weight = 35252.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073177 restraints weight = 20093.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073746 restraints weight = 14705.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.074295 restraints weight = 14258.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.074298 restraints weight = 12185.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14392  Z= 0.222
  Angle     :  0.593  10.876  19534  Z= 0.305
  Chirality :  0.045   0.211   2112
  Planarity :  0.003   0.035   2514
  Dihedral  :  4.669  46.996   1895
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.29 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.54 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.22), residues: 1700
  helix: -0.39 (0.36), residues: 236
  sheet:  0.01 (0.30), residues: 338
  loop : -1.11 (0.20), residues: 1126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 886 
 TYR   0.017   0.001   TYR A 507 
 PHE   0.016   0.002   PHE A 565 
 TRP   0.028   0.002   TRP A 833 
 HIS   0.005   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (14352)
  covalent geometry    : angle       0.59237 (19454)
  SS BOND              : bond        0.00341 (   40)
  SS BOND              : angle       0.76134 (   80)
  hydrogen bonds       : bond        0.04157 (  329)
  hydrogen bonds       : angle       5.38979 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6469 (m-10) cc_final: 0.5977 (m-80)
REVERT: A  777 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6618 (m-10)
REVERT: A  898 TRP cc_start: 0.7920 (m100) cc_final: 0.7548 (m100)
REVERT: B  646 TYR cc_start: 0.6186 (m-10) cc_final: 0.5636 (m-80)
REVERT: B  807 MET cc_start: 0.8182 (mmm) cc_final: 0.7870 (mmm)
REVERT: C   70 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7993 (pm20)
REVERT: D   70 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7693 (pm20)
  outliers start: 22
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0761
  time to fit residues: 10.3355
Evaluate side-chains
  75 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  777 PHE
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   70 GLN
Chi-restraints excluded: chain D residue   70 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 128 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 162 optimal weight:    3.9990
   chunk 141 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0470
   chunk 42 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.3482

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.111900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.074961 restraints weight = 35163.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.075697 restraints weight = 19558.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.075429 restraints weight = 14979.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.075892 restraints weight = 14422.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.076046 restraints weight = 13643.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14392  Z= 0.157
  Angle     :  0.569  11.497  19534  Z= 0.292
  Chirality :  0.044   0.208   2112
  Planarity :  0.003   0.035   2514
  Dihedral  :  4.612  46.933   1895
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.18 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.11 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.22), residues: 1700
  helix: -0.34 (0.36), residues: 234
  sheet:  0.03 (0.30), residues: 338
  loop : -1.09 (0.20), residues: 1128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 888 
 TYR   0.018   0.001   TYR A 579 
 PHE   0.017   0.001   PHE B 706 
 TRP   0.029   0.001   TRP A 833 
 HIS   0.005   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (14352)
  covalent geometry    : angle       0.56873 (19454)
  SS BOND              : bond        0.00287 (   40)
  SS BOND              : angle       0.67812 (   80)
  hydrogen bonds       : bond        0.03967 (  329)
  hydrogen bonds       : angle       5.32277 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6451 (m-10) cc_final: 0.6050 (m-80)
REVERT: A  777 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6628 (m-10)
REVERT: A  898 TRP cc_start: 0.7428 (m100) cc_final: 0.7156 (m100)
REVERT: B  646 TYR cc_start: 0.6229 (m-10) cc_final: 0.5664 (m-80)
REVERT: B  807 MET cc_start: 0.8065 (mmm) cc_final: 0.7829 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0840
  time to fit residues: 11.5765
Evaluate side-chains
  77 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  777 PHE
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 151 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 136 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 128 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 79 optimal weight:   30.0000
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 622 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.112880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.072355 restraints weight = 36814.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.074091 restraints weight = 21027.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.075408 restraints weight = 13843.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.075810 restraints weight = 11480.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.075848 restraints weight = 10706.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  14392  Z= 0.243
  Angle     :  0.630  12.329  19534  Z= 0.321
  Chirality :  0.045   0.215   2112
  Planarity :  0.004   0.035   2514
  Dihedral  :  4.854  46.483   1895
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.06 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.92 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.21), residues: 1700
  helix: -0.43 (0.36), residues: 234
  sheet: -0.16 (0.30), residues: 350
  loop : -1.18 (0.20), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.019   0.002   TYR A 507 
 PHE   0.018   0.002   PHE B 565 
 TRP   0.031   0.002   TRP A 833 
 HIS   0.004   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (14352)
  covalent geometry    : angle       0.62838 (19454)
  SS BOND              : bond        0.00386 (   40)
  SS BOND              : angle       0.86067 (   80)
  hydrogen bonds       : bond        0.04362 (  329)
  hydrogen bonds       : angle       5.45762 (  873)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  646 TYR cc_start: 0.6510 (m-10) cc_final: 0.5850 (m-80)
REVERT: A  777 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7081 (m-10)
REVERT: A  898 TRP cc_start: 0.8550 (m100) cc_final: 0.8069 (m100)
REVERT: B  442 MET cc_start: 0.9413 (mmm) cc_final: 0.8973 (tpt)
REVERT: B  646 TYR cc_start: 0.6017 (m-10) cc_final: 0.5316 (m-80)
REVERT: B  807 MET cc_start: 0.8589 (mmm) cc_final: 0.8363 (mmm)
  outliers start: 24
  outliers final: 18
  residues processed: 79
  average time/residue: 0.0972
  time to fit residues: 12.7405
Evaluate side-chains
  75 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  686 CYS
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  777 PHE
Chi-restraints excluded: chain A residue  796 CYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  796 CYS
Chi-restraints excluded: chain B residue  905 TYR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   70 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 166 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 125 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0870
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.114847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.073531 restraints weight = 36444.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.076306 restraints weight = 17636.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.078046 restraints weight = 11882.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.079071 restraints weight = 9564.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.079702 restraints weight = 8447.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14392  Z= 0.110
  Angle     :  0.573  12.322  19534  Z= 0.292
  Chirality :  0.044   0.203   2112
  Planarity :  0.003   0.034   2514
  Dihedral  :  4.617  46.735   1895
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.06 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 15.55 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.22), residues: 1700
  helix: -0.34 (0.36), residues: 234
  sheet:  0.08 (0.30), residues: 338
  loop : -1.09 (0.20), residues: 1128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  47 
 TYR   0.019   0.001   TYR B 579 
 PHE   0.020   0.001   PHE B 706 
 TRP   0.030   0.001   TRP A 833 
 HIS   0.005   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (14352)
  covalent geometry    : angle       0.57227 (19454)
  SS BOND              : bond        0.00245 (   40)
  SS BOND              : angle       0.63789 (   80)
  hydrogen bonds       : bond        0.03825 (  329)
  hydrogen bonds       : angle       5.28119 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2232.59 seconds
wall clock time: 39 minutes 18.65 seconds (2358.65 seconds total)