Starting phenix.real_space_refine
on Fri May 16 09:32:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yyt_39678/05_2025/8yyt_39678.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     117      5.16       5
     C    8962      2.51       5
     N    2443      2.21       5
     O    2625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14147
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 6337
          Classifications: {'peptide': 785}
          Link IDs: {'PTRANS': 41, 'TRANS': 743}
          Chain breaks: 20
    Chain: "B"
      Number of atoms: 6358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 788, 6358
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 41, 'TRANS': 746}
          Chain breaks: 17
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 363
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 45}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 363
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 45}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 363
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 45}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 363
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 45}
          Chain breaks: 1
  Time building chain proxies: 8.85, per 1000 atoms: 0.63
  Number of scatterers: 14147
  At special positions: 0
  Unit cell: (125.4, 125.4, 165, 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     117     16.00
     O    2625      8.00
     N    2443      7.00
     C    8962      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=40, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 153 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 219 " - pdb=" SG  CYS A 228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 223 " - pdb=" SG  CYS A 234 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 235 " - pdb=" SG  CYS A 243 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 239 " - pdb=" SG  CYS A 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 286 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 293 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 328 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 674 " - pdb=" SG  CYS A 887 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 813 " - pdb=" SG  CYS A 822 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  35 " - pdb=" SG  CYS B  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 153 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - pdb=" SG  CYS B 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 219 " - pdb=" SG  CYS B 228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 223 " - pdb=" SG  CYS B 234 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 235 " - pdb=" SG  CYS B 243 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 239 " - pdb=" SG  CYS B 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 255 " - pdb=" SG  CYS B 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 268 " - pdb=" SG  CYS B 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 286 " - pdb=" SG  CYS B 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 293 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 315 " - pdb=" SG  CYS B 328 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 339 " - pdb=" SG  CYS B 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 674 " - pdb=" SG  CYS B 887 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 813 " - pdb=" SG  CYS B 822 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   7 " - pdb=" SG  CYS E  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  19 " - pdb=" SG  CYS E  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   7 " - pdb=" SG  CYS F  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  19 " - pdb=" SG  CYS F  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  36 " - pdb=" SG  CYS F  41 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.37
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3298

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 29 sheets defined
      16.3% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 282 through 297
      removed outlier: 3.537A  pdb=" N   CYS A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LYS A 294 " --> pdb=" O   HIS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 343
      No H-bonds generated for 'chain 'A' and resid 341 through 343'
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 356 through 358
      No H-bonds generated for 'chain 'A' and resid 356 through 358'
    Processing helix  chain 'A' and resid 378 through 386
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.617A  pdb=" N   ILE A 466 " --> pdb=" O   CYS A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 670
      removed outlier: 3.561A  pdb=" N   GLU A 670 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 741
      removed outlier: 3.513A  pdb=" N   ARG A 729 " --> pdb=" O   GLU A 725 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 733 " --> pdb=" O   ARG A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 897
    Processing helix  chain 'B' and resid 175 through 180
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 282 through 297
      removed outlier: 3.537A  pdb=" N   CYS B 286 " --> pdb=" O   ASN B 282 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS B 294 " --> pdb=" O   HIS B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 356 through 358
      No H-bonds generated for 'chain 'B' and resid 356 through 358'
    Processing helix  chain 'B' and resid 378 through 386
    Processing helix  chain 'B' and resid 462 through 473
      removed outlier: 3.606A  pdb=" N   ILE B 466 " --> pdb=" O   CYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 670
      removed outlier: 3.562A  pdb=" N   GLU B 670 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 741
      removed outlier: 3.706A  pdb=" N   PHE B 728 " --> pdb=" O   GLU B 724 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B 729 " --> pdb=" O   GLU B 725 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 897
    Processing helix  chain 'C' and resid 9 through 15
      removed outlier: 3.665A  pdb=" N   GLU C  13 " --> pdb=" O   SER C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 18
      No H-bonds generated for 'chain 'C' and resid 16 through 18'
    Processing helix  chain 'C' and resid 32 through 37
    Processing helix  chain 'C' and resid 42 through 47
      removed outlier: 4.046A  pdb=" N   GLU C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 51
    Processing helix  chain 'D' and resid 9 through 16
      removed outlier: 3.624A  pdb=" N   GLU D  13 " --> pdb=" O   SER D   9 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   TYR D  16 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 37
    Processing helix  chain 'D' and resid 42 through 47
      removed outlier: 4.043A  pdb=" N   GLU D  47 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 51
    Processing helix  chain 'E' and resid 8 through 20
      removed outlier: 4.541A  pdb=" N   TYR E  16 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU E  17 " --> pdb=" O   GLU E  13 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL E  18 " --> pdb=" O   ALA E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 37
    Processing helix  chain 'E' and resid 42 through 47
    Processing helix  chain 'F' and resid 8 through 20
      removed outlier: 4.631A  pdb=" N   TYR F  16 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LEU F  17 " --> pdb=" O   GLU F  13 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   VAL F  18 " --> pdb=" O   ALA F  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 37
    Processing helix  chain 'F' and resid 42 through 47
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40
      removed outlier: 5.941A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   PHE A  91 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   ILE A  62 " --> pdb=" O   PHE A  91 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU A  88 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   PHE A 123 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A  90 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84
    Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201
    Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 307
      removed outlier: 3.725A  pdb=" N   ILE A 312 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348
    Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363
    Processing sheet with id=AA8, first strand: chain 'A' and resid 504 through 507
    Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 561
      removed outlier: 3.534A  pdb=" N   TYR A 534 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY A 529 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 626 through 626
    Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 626
    Processing sheet with id=AB3, first strand: chain 'A' and resid 786 through 789
      removed outlier: 3.639A  pdb=" N   TYR A 806 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 830 " --> pdb=" O   TYR A 806 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 846 through 849
      removed outlier: 3.549A  pdb=" N   THR A 846 " --> pdb=" O   MET A 858 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL A 855 " --> pdb=" O   LEU A 901 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 883 through 889
      removed outlier: 3.806A  pdb=" N   LEU A 871 " --> pdb=" O   THR A 916 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE A 913 " --> pdb=" O   TRP A 924 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   TRP A 924 " --> pdb=" O   ILE A 913 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   ALA A 915 " --> pdb=" O   GLY A 922 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 883 through 889
      removed outlier: 3.806A  pdb=" N   LEU A 871 " --> pdb=" O   THR A 916 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 40
      removed outlier: 6.027A  pdb=" N   LEU B  60 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   PHE B  91 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ILE B  62 " --> pdb=" O   PHE B  91 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU B  88 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   PHE B 123 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU B  90 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AB9, first strand: chain 'B' and resid 198 through 201
    Processing sheet with id=AC1, first strand: chain 'B' and resid 305 through 307
      removed outlier: 3.727A  pdb=" N   ILE B 312 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 319 through 320
    Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 348
    Processing sheet with id=AC4, first strand: chain 'B' and resid 362 through 363
    Processing sheet with id=AC5, first strand: chain 'B' and resid 504 through 507
    Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 561
      removed outlier: 3.545A  pdb=" N   TYR B 534 " --> pdb=" O   THR B 557 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY B 529 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 626 through 631
      removed outlier: 5.132A  pdb=" N   ASP B 627 " --> pdb=" O   LYS B 643 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LYS B 643 " --> pdb=" O   ASP B 627 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 795 " --> pdb=" O   LEU B 640 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 786 through 789
      removed outlier: 3.638A  pdb=" N   TYR B 806 " --> pdb=" O   ALA B 830 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA B 830 " --> pdb=" O   TYR B 806 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 846 through 849
      removed outlier: 3.557A  pdb=" N   THR B 846 " --> pdb=" O   MET B 858 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL B 855 " --> pdb=" O   LEU B 901 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 883 through 889
      removed outlier: 3.810A  pdb=" N   LEU B 871 " --> pdb=" O   THR B 916 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ILE B 913 " --> pdb=" O   TRP B 924 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   TRP B 924 " --> pdb=" O   ILE B 913 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   ALA B 915 " --> pdb=" O   GLY B 922 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 883 through 889
      removed outlier: 3.810A  pdb=" N   LEU B 871 " --> pdb=" O   THR B 916 " (cutoff:3.500A)

    341 hydrogen bonds defined for protein.
    897 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: 4.47

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4633
        1.35 -     1.47: 3447
        1.47 -     1.59: 6235
        1.59 -     1.70: 0
        1.70 -     1.82: 138
  Bond restraints: 14453
  Sorted by residual:
  bond pdb=" C   ARG B 436 "
       pdb=" N   GLN B 437 "
    ideal  model  delta    sigma   weight residual
    1.332  1.318  0.014 1.40e-02 5.10e+03 1.07e+00
  bond pdb=" CB  PRO B 270 "
       pdb=" CG  PRO B 270 "
    ideal  model  delta    sigma   weight residual
    1.492  1.440  0.052 5.00e-02 4.00e+02 1.07e+00
  bond pdb=" CB  ASP B 431 "
       pdb=" CG  ASP B 431 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.04e+00
  bond pdb=" CB  PRO A 270 "
       pdb=" CG  PRO A 270 "
    ideal  model  delta    sigma   weight residual
    1.492  1.441  0.051 5.00e-02 4.00e+02 1.03e+00
  bond pdb=" C   GLU B 864 "
       pdb=" N   PRO B 865 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.023 2.34e-02 1.83e+03 9.26e-01
  ... (remaining 14448 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 19165
        2.12 -     4.24: 317
        4.24 -     6.35: 44
        6.35 -     8.47: 5
        8.47 -    10.59: 6
  Bond angle restraints: 19537
  Sorted by residual:
  angle pdb=" C   VAL E  12 "
        pdb=" N   GLU E  13 "
        pdb=" CA  GLU E  13 "
      ideal   model   delta    sigma   weight residual
     122.54  116.24    6.30 1.65e+00 3.67e-01 1.46e+01
  angle pdb=" CB  MET A  83 "
        pdb=" CG  MET A  83 "
        pdb=" SD  MET A  83 "
      ideal   model   delta    sigma   weight residual
     112.70  123.29  -10.59 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" CB  MET B  83 "
        pdb=" CG  MET B  83 "
        pdb=" SD  MET B  83 "
      ideal   model   delta    sigma   weight residual
     112.70  123.10  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  LYS B  67 "
        pdb=" CB  LYS B  67 "
        pdb=" CG  LYS B  67 "
      ideal   model   delta    sigma   weight residual
     114.10  120.28   -6.18 2.00e+00 2.50e-01 9.54e+00
  angle pdb=" CA  LYS A  67 "
        pdb=" CB  LYS A  67 "
        pdb=" CG  LYS A  67 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.40e+00
  ... (remaining 19532 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 7502
       18.03 -    36.07: 939
       36.07 -    54.10: 224
       54.10 -    72.13: 36
       72.13 -    90.17: 26
  Dihedral angle restraints: 8727
    sinusoidal: 3639
      harmonic: 5088
  Sorted by residual:
  dihedral pdb=" CB  CYS F  36 "
           pdb=" SG  CYS F  36 "
           pdb=" SG  CYS F  41 "
           pdb=" CB  CYS F  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.17   90.17     1      1.00e+01 1.00e-02 9.63e+01
  dihedral pdb=" CB  CYS E  36 "
           pdb=" SG  CYS E  36 "
           pdb=" SG  CYS E  41 "
           pdb=" CB  CYS E  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.94  -90.06     1      1.00e+01 1.00e-02 9.61e+01
  dihedral pdb=" CB  CYS C  36 "
           pdb=" SG  CYS C  36 "
           pdb=" SG  CYS C  41 "
           pdb=" CB  CYS C  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.98   70.02     1      1.00e+01 1.00e-02 6.32e+01
  ... (remaining 8724 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1568
       0.044 -    0.087: 391
       0.087 -    0.130: 161
       0.130 -    0.174: 9
       0.174 -    0.217: 1
  Chirality restraints: 2130
  Sorted by residual:
  chirality pdb=" CB  VAL E  12 "
            pdb=" CA  VAL E  12 "
            pdb=" CG1 VAL E  12 "
            pdb=" CG2 VAL E  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CG  LEU B 528 "
            pdb=" CB  LEU B 528 "
            pdb=" CD1 LEU B 528 "
            pdb=" CD2 LEU B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CG  LEU A 528 "
            pdb=" CB  LEU A 528 "
            pdb=" CD1 LEU A 528 "
            pdb=" CD2 LEU A 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 2127 not shown)

  Planarity restraints: 2512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 269 "   -0.046 5.00e-02 4.00e+02   6.84e-02 7.48e+00
        pdb=" N   PRO A 270 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 270 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 270 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 269 "    0.046 5.00e-02 4.00e+02   6.81e-02 7.42e+00
        pdb=" N   PRO B 270 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 268 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO B 269 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 269 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 269 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 2509 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1032
        2.74 -     3.28: 14427
        3.28 -     3.82: 23630
        3.82 -     4.36: 27358
        4.36 -     4.90: 45460
  Nonbonded interactions: 111907
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 802 "
            pdb=" OG1 THR A 832 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   HIS B 802 "
            pdb=" OG1 THR B 832 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NZ  LYS A 294 "
            pdb=" OD1 ASN A 295 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" NZ  LYS B 294 "
            pdb=" OD1 ASN B 295 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   ASP B 734 "
            pdb=" ND2 ASN B 738 "
     model   vdw
     2.265 3.120
  ... (remaining 111902 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 28 through 454 or resid 456 through 934))
  selection = (chain 'B' and (resid 28 through 124 or resid 126 through 430 or resid 433 throu \ 
gh 437 or resid 439 through 626 or resid 628 through 934))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.170
  Process input model:                     33.490
  Find NCS groups from input model:        0.590
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
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   0.052  14493  Z= 0.125
  Angle     :  0.684  10.591  19617  Z= 0.354
  Chirality :  0.043   0.217   2130
  Planarity :  0.005   0.089   2512
  Dihedral  : 16.574  85.474   5309
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  : 25.64 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.21), residues: 1663
  helix: -1.75 (0.33), residues: 213
  sheet: -0.67 (0.28), residues: 315
  loop : -1.09 (0.19), residues: 1135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 642 
 HIS   0.004   0.001   HIS A 456 
 PHE   0.014   0.001   PHE A 732 
 TYR   0.029   0.001   TYR B 401 
 ARG   0.010   0.000   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26585 (  313)
  hydrogen bonds       : angle      10.62398 (  897)
  SS BOND              : bond        0.00162 (   40)
  SS BOND              : angle       0.71973 (   80)
  covalent geometry    : bond        0.00273 (14453)
  covalent geometry    : angle       0.68389 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  833 MET cc_start: 0.8765 (pmm) cc_final: 0.8519 (pmm)
REVERT: B  833 MET cc_start: 0.8870 (pmm) cc_final: 0.8630 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2743
  time to fit residues: 26.7476
Evaluate side-chains
  60 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 134 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 156 optimal weight:    0.0980
   overall best weight:    3.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 434 ASN
A 654 HIS
B 214 HIS
** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 654 HIS
C  51 ASN
D  51 ASN
F   4 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.125673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.100306 restraints weight = 82727.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.101636 restraints weight = 51198.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.102636 restraints weight = 38976.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  14493  Z= 0.238
  Angle     :  0.691   7.553  19617  Z= 0.359
  Chirality :  0.046   0.167   2130
  Planarity :  0.005   0.065   2512
  Dihedral  :  5.126  39.859   1894
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 22.19 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.21), residues: 1663
  helix: -1.35 (0.35), residues: 214
  sheet: -0.35 (0.29), residues: 292
  loop : -1.14 (0.19), residues: 1157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 578 
 HIS   0.004   0.001   HIS B 654 
 PHE   0.021   0.002   PHE B 658 
 TYR   0.021   0.002   TYR B 171 
 ARG   0.004   0.001   ARG B 784 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  313)
  hydrogen bonds       : angle       7.20844 (  897)
  SS BOND              : bond        0.00389 (   40)
  SS BOND              : angle       0.79392 (   80)
  covalent geometry    : bond        0.00535 (14453)
  covalent geometry    : angle       0.69043 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 58
  time to evaluate  : 1.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8108 (tpp) cc_final: 0.7869 (tpp)
REVERT: A  321 MET cc_start: 0.8427 (ppp) cc_final: 0.8175 (ppp)
REVERT: A  368 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8864 (pp)
REVERT: A  470 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8127 (tp30)
REVERT: A  531 MET cc_start: 0.8731 (pmm) cc_final: 0.8518 (pmm)
REVERT: B   83 MET cc_start: 0.7999 (tpp) cc_final: 0.7793 (tpp)
REVERT: B  321 MET cc_start: 0.8354 (ppp) cc_final: 0.8125 (ppp)
REVERT: B  368 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8857 (pp)
REVERT: B  531 MET cc_start: 0.8752 (pmm) cc_final: 0.8549 (pmm)
REVERT: B  736 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9441 (tp)
REVERT: F    4 GLN cc_start: 0.2091 (OUTLIER) cc_final: 0.1626 (tt0)
  outliers start: 65
  outliers final: 35
  residues processed: 122
  average time/residue: 0.2497
  time to fit residues: 46.8530
Evaluate side-chains
  95 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 55
  time to evaluate  : 1.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  593 VAL
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain F residue    4 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 58 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 124 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 71 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 325 ASN
B 325 ASN
F   4 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.122128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.097211 restraints weight = 85858.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.098692 restraints weight = 52014.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.099665 restraints weight = 38359.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14493  Z= 0.121
  Angle     :  0.591   8.894  19617  Z= 0.306
  Chirality :  0.043   0.143   2130
  Planarity :  0.004   0.067   2512
  Dihedral  :  4.898  41.116   1894
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.32 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.21), residues: 1663
  helix: -1.09 (0.35), residues: 212
  sheet: -0.75 (0.27), residues: 350
  loop : -0.97 (0.20), residues: 1101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 439 
 HIS   0.004   0.001   HIS D   5 
 PHE   0.016   0.001   PHE B 658 
 TYR   0.013   0.001   TYR B 457 
 ARG   0.005   0.000   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  313)
  hydrogen bonds       : angle       6.64032 (  897)
  SS BOND              : bond        0.00243 (   40)
  SS BOND              : angle       0.61259 (   80)
  covalent geometry    : bond        0.00278 (14453)
  covalent geometry    : angle       0.59046 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 60
  time to evaluate  : 1.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8528 (tm-30)
REVERT: A  470 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8078 (tp30)
REVERT: B  382 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8529 (tm-30)
REVERT: B  470 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8061 (tp30)
REVERT: B  643 LYS cc_start: 0.9672 (mmtm) cc_final: 0.9399 (ptmm)
REVERT: B  736 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9436 (tp)
REVERT: F   11 LEU cc_start: 0.7795 (mp) cc_final: 0.7285 (mp)
  outliers start: 44
  outliers final: 26
  residues processed: 103
  average time/residue: 0.2607
  time to fit residues: 40.7560
Evaluate side-chains
  87 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 56
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  470 GLU
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   13 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 121 optimal weight:    0.3980
   chunk 78 optimal weight:   10.0000
   chunk 153 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 161 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9980
   chunk 146 optimal weight:   10.0000
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.121803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.096907 restraints weight = 85890.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.098356 restraints weight = 51683.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.099332 restraints weight = 37949.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14493  Z= 0.123
  Angle     :  0.576   7.533  19617  Z= 0.297
  Chirality :  0.043   0.154   2130
  Planarity :  0.005   0.096   2512
  Dihedral  :  4.798  41.393   1894
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.82 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.21), residues: 1663
  helix: -0.91 (0.35), residues: 222
  sheet: -0.80 (0.26), residues: 365
  loop : -0.91 (0.20), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 439 
 HIS   0.003   0.000   HIS C   5 
 PHE   0.014   0.001   PHE B 658 
 TYR   0.012   0.001   TYR B 457 
 ARG   0.004   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  313)
  hydrogen bonds       : angle       6.27658 (  897)
  SS BOND              : bond        0.00202 (   40)
  SS BOND              : angle       0.57204 (   80)
  covalent geometry    : bond        0.00280 (14453)
  covalent geometry    : angle       0.57599 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 59
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8635 (tm-30)
REVERT: A  470 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8093 (tp30)
REVERT: A  531 MET cc_start: 0.8834 (pmm) cc_final: 0.8529 (pmm)
REVERT: A  580 MET cc_start: 0.9485 (pmm) cc_final: 0.9098 (pmm)
REVERT: A  659 TRP cc_start: 0.6011 (OUTLIER) cc_final: 0.5551 (p90)
REVERT: B  382 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8540 (tm-30)
REVERT: B  531 MET cc_start: 0.8849 (pmm) cc_final: 0.8591 (pmm)
REVERT: B  659 TRP cc_start: 0.6029 (OUTLIER) cc_final: 0.5518 (p90)
REVERT: B  736 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9432 (tp)
  outliers start: 57
  outliers final: 32
  residues processed: 113
  average time/residue: 0.2683
  time to fit residues: 45.5446
Evaluate side-chains
  95 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 57
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain F residue   41 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 43 optimal weight:    0.1980
   chunk 171 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 129 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:   30.0000
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  51 ASN ** 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 = 0.4404 r_free = 0.4404 target = 0.124038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.098732 restraints weight = 79358.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.100077 restraints weight = 50566.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.100991 restraints weight = 38546.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14493  Z= 0.122
  Angle     :  0.574   8.689  19617  Z= 0.294
  Chirality :  0.043   0.245   2130
  Planarity :  0.004   0.064   2512
  Dihedral  :  4.726  41.560   1894
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.82 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.21), residues: 1663
  helix: -0.82 (0.35), residues: 222
  sheet: -0.53 (0.26), residues: 353
  loop : -0.92 (0.20), residues: 1088

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 439 
 HIS   0.005   0.001   HIS D  10 
 PHE   0.013   0.001   PHE B 658 
 TYR   0.018   0.001   TYR B 872 
 ARG   0.003   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  313)
  hydrogen bonds       : angle       6.06608 (  897)
  SS BOND              : bond        0.00190 (   40)
  SS BOND              : angle       0.58386 (   80)
  covalent geometry    : bond        0.00283 (14453)
  covalent geometry    : angle       0.57416 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 61
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8640 (tm-30)
REVERT: B  382 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8649 (tm-30)
REVERT: B  733 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8284 (mm-30)
REVERT: B  736 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9439 (tp)
  outliers start: 63
  outliers final: 39
  residues processed: 120
  average time/residue: 0.2953
  time to fit residues: 51.2132
Evaluate side-chains
  101 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 58
  time to evaluate  : 1.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  786 PHE
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  786 PHE
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain E residue   13 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   chunk 77 optimal weight:   40.0000
   chunk 43 optimal weight:    0.0770
   chunk 144 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 170 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.6144

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS
** D  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.119944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.094808 restraints weight = 88462.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.096265 restraints weight = 53170.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.097259 restraints weight = 39031.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  14493  Z= 0.192
  Angle     :  0.646  12.101  19617  Z= 0.327
  Chirality :  0.044   0.301   2130
  Planarity :  0.004   0.061   2512
  Dihedral  :  4.965  42.384   1894
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 24.64 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.21), residues: 1663
  helix: -0.81 (0.36), residues: 222
  sheet: -0.40 (0.27), residues: 343
  loop : -1.02 (0.20), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 578 
 HIS   0.004   0.001   HIS B 456 
 PHE   0.013   0.002   PHE A 533 
 TYR   0.016   0.001   TYR A 534 
 ARG   0.015   0.000   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  313)
  hydrogen bonds       : angle       6.08525 (  897)
  SS BOND              : bond        0.00309 (   40)
  SS BOND              : angle       0.68547 (   80)
  covalent geometry    : bond        0.00438 (14453)
  covalent geometry    : angle       0.64606 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 60
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8657 (tm-30)
REVERT: A  531 MET cc_start: 0.8859 (pmm) cc_final: 0.8565 (pmm)
REVERT: A  659 TRP cc_start: 0.6150 (OUTLIER) cc_final: 0.5312 (p90)
REVERT: B  382 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8649 (tm-30)
REVERT: B  659 TRP cc_start: 0.5985 (OUTLIER) cc_final: 0.5210 (p90)
REVERT: B  733 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8354 (mm-30)
REVERT: B  736 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9452 (tp)
REVERT: D   45 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8928 (pm20)
  outliers start: 63
  outliers final: 42
  residues processed: 118
  average time/residue: 0.2931
  time to fit residues: 50.4449
Evaluate side-chains
  105 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 56
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  786 PHE
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  524 PHE
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  786 PHE
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain E residue   13 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 165 optimal weight:    4.9990
   chunk 171 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 127 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 130 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 458 ASN
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.120741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.095826 restraints weight = 86967.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.097313 restraints weight = 52173.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.098304 restraints weight = 38024.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14493  Z= 0.121
  Angle     :  0.600  11.584  19617  Z= 0.303
  Chirality :  0.043   0.306   2130
  Planarity :  0.004   0.059   2512
  Dihedral  :  4.865  43.213   1894
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.76 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.21), residues: 1663
  helix: -0.61 (0.37), residues: 210
  sheet: -0.43 (0.27), residues: 348
  loop : -0.86 (0.20), residues: 1105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 439 
 HIS   0.007   0.001   HIS A 456 
 PHE   0.017   0.001   PHE A 283 
 TYR   0.021   0.001   TYR B 118 
 ARG   0.004   0.000   ARG A 729 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03229 (  313)
  hydrogen bonds       : angle       5.99546 (  897)
  SS BOND              : bond        0.00194 (   40)
  SS BOND              : angle       0.58019 (   80)
  covalent geometry    : bond        0.00282 (14453)
  covalent geometry    : angle       0.60010 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 58
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8674 (tm-30)
REVERT: A  531 MET cc_start: 0.8850 (pmm) cc_final: 0.8587 (pmm)
REVERT: A  659 TRP cc_start: 0.6081 (OUTLIER) cc_final: 0.5376 (p90)
REVERT: B  382 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8688 (tm-30)
REVERT: B  659 TRP cc_start: 0.5973 (OUTLIER) cc_final: 0.5229 (p90)
REVERT: B  733 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8268 (mm-30)
REVERT: B  736 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9448 (tp)
  outliers start: 58
  outliers final: 40
  residues processed: 111
  average time/residue: 0.2744
  time to fit residues: 45.0007
Evaluate side-chains
  101 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 55
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  786 PHE
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  861 GLU
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  786 PHE
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain E residue   13 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 167 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0470
   chunk 140 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 114 optimal weight:    0.0000
   chunk 156 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 162 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9980
   overall best weight:    0.5682

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

Flipped N/Q/H residues before XYZ refinement:
A 291 HIS
** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.130854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.102185 restraints weight = 63457.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.103360 restraints weight = 45694.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.104055 restraints weight = 37460.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  14493  Z= 0.100
  Angle     :  0.599  10.011  19617  Z= 0.300
  Chirality :  0.043   0.250   2130
  Planarity :  0.004   0.059   2512
  Dihedral  :  4.764  43.082   1894
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 25.08 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.21), residues: 1663
  helix: -0.57 (0.37), residues: 210
  sheet: -0.34 (0.27), residues: 350
  loop : -0.83 (0.20), residues: 1103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 439 
 HIS   0.003   0.000   HIS D   5 
 PHE   0.015   0.001   PHE A 283 
 TYR   0.015   0.001   TYR B 118 
 ARG   0.014   0.000   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03131 (  313)
  hydrogen bonds       : angle       5.86420 (  897)
  SS BOND              : bond        0.00135 (   40)
  SS BOND              : angle       0.54391 (   80)
  covalent geometry    : bond        0.00235 (14453)
  covalent geometry    : angle       0.59915 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 53
  time to evaluate  : 1.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8561 (tm-30)
REVERT: A  531 MET cc_start: 0.8707 (pmm) cc_final: 0.8421 (pmm)
REVERT: B  382 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8572 (tm-30)
REVERT: B  531 MET cc_start: 0.8623 (pmm) cc_final: 0.8321 (pmm)
REVERT: B  659 TRP cc_start: 0.6121 (OUTLIER) cc_final: 0.5678 (p90)
  outliers start: 52
  outliers final: 34
  residues processed: 105
  average time/residue: 0.2521
  time to fit residues: 41.4254
Evaluate side-chains
  90 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 53
  time to evaluate  : 1.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  293 CYS
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  861 GLU
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  861 GLU
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain E residue   13 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 121 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 139 optimal weight:    9.9990
   chunk 165 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 155 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.119902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.094805 restraints weight = 85755.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.096227 restraints weight = 52541.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.097169 restraints weight = 39030.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085  14493  Z= 0.267
  Angle     :  0.715  10.782  19617  Z= 0.360
  Chirality :  0.046   0.201   2130
  Planarity :  0.005   0.062   2512
  Dihedral  :  5.205  43.770   1894
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 25.20 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.21), residues: 1663
  helix: -0.48 (0.38), residues: 211
  sheet: -0.30 (0.27), residues: 337
  loop : -0.99 (0.20), residues: 1115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 439 
 HIS   0.006   0.001   HIS B 456 
 PHE   0.023   0.002   PHE B 455 
 TYR   0.022   0.002   TYR A 425 
 ARG   0.007   0.001   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  313)
  hydrogen bonds       : angle       5.99102 (  897)
  SS BOND              : bond        0.00433 (   40)
  SS BOND              : angle       0.82775 (   80)
  covalent geometry    : bond        0.00597 (14453)
  covalent geometry    : angle       0.71411 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 57
  time to evaluate  : 1.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8629 (tm-30)
REVERT: A  390 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7784 (pm20)
REVERT: A  428 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7660 (t80)
REVERT: A  531 MET cc_start: 0.8873 (pmm) cc_final: 0.8598 (pmm)
REVERT: B  382 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8635 (tm-30)
REVERT: B  390 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7776 (pm20)
REVERT: B  531 MET cc_start: 0.8855 (pmm) cc_final: 0.8549 (pmm)
REVERT: B  580 MET cc_start: 0.9172 (pmm) cc_final: 0.8935 (pmm)
REVERT: B  659 TRP cc_start: 0.6058 (OUTLIER) cc_final: 0.5180 (p90)
REVERT: B  733 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8471 (mm-30)
REVERT: B  858 MET cc_start: -0.5923 (tpt) cc_final: -0.6231 (tpt)
  outliers start: 50
  outliers final: 40
  residues processed: 106
  average time/residue: 0.2345
  time to fit residues: 38.9484
Evaluate side-chains
  99 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 52
  time to evaluate  : 1.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  293 CYS
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  390 GLU
Chi-restraints excluded: chain A residue  428 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  524 PHE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  786 PHE
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  861 GLU
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  390 GLU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain B residue  925 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 155 optimal weight:   20.0000
   chunk 52 optimal weight:    8.9990
   chunk 81 optimal weight:    0.8980
   chunk 132 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
D  48 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.120968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.096307 restraints weight = 83246.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.097637 restraints weight = 51427.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.098545 restraints weight = 38135.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14493  Z= 0.142
  Angle     :  0.633  11.050  19617  Z= 0.315
  Chirality :  0.044   0.195   2130
  Planarity :  0.004   0.061   2512
  Dihedral  :  5.037  45.276   1894
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.71 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.21), residues: 1663
  helix: -0.45 (0.38), residues: 211
  sheet: -0.29 (0.27), residues: 341
  loop : -0.92 (0.20), residues: 1111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 439 
 HIS   0.004   0.001   HIS C   5 
 PHE   0.012   0.001   PHE B 658 
 TYR   0.013   0.001   TYR A 872 
 ARG   0.005   0.000   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  313)
  hydrogen bonds       : angle       5.90700 (  897)
  SS BOND              : bond        0.00236 (   40)
  SS BOND              : angle       0.65283 (   80)
  covalent geometry    : bond        0.00330 (14453)
  covalent geometry    : angle       0.63270 (19537)

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

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

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3326 Ramachandran restraints generated.
    1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 53
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8646 (tm-30)
REVERT: A  531 MET cc_start: 0.8789 (pmm) cc_final: 0.8521 (pmm)
REVERT: A  659 TRP cc_start: 0.5986 (OUTLIER) cc_final: 0.5001 (p90)
REVERT: B  382 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8672 (tm-30)
REVERT: B  390 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7730 (pm20)
REVERT: B  580 MET cc_start: 0.9126 (pmm) cc_final: 0.8887 (pmm)
REVERT: B  659 TRP cc_start: 0.5835 (OUTLIER) cc_final: 0.4989 (p90)
REVERT: B  858 MET cc_start: -0.5952 (tpt) cc_final: -0.6282 (tpt)
  outliers start: 44
  outliers final: 37
  residues processed: 95
  average time/residue: 0.2441
  time to fit residues: 36.1263
Evaluate side-chains
  95 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 53
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  293 CYS
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  659 TRP
Chi-restraints excluded: chain A residue  786 PHE
Chi-restraints excluded: chain A residue  813 CYS
Chi-restraints excluded: chain A residue  861 GLU
Chi-restraints excluded: chain A residue  876 TYR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  358 ARG
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  390 GLU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  524 PHE
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  659 TRP
Chi-restraints excluded: chain B residue  729 ARG
Chi-restraints excluded: chain B residue  786 PHE
Chi-restraints excluded: chain B residue  813 CYS
Chi-restraints excluded: chain B residue  876 TYR
Chi-restraints excluded: chain B residue  925 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 170 optimal weight:    0.1980
   chunk 157 optimal weight:    0.0040
   chunk 125 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 127 optimal weight:    9.9990
   chunk 136 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0020
   overall best weight:    0.3802

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

Flipped N/Q/H residues before XYZ refinement:
A 866 ASN
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.138791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.108340 restraints weight = 83981.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.109226 restraints weight = 51283.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.109962 restraints weight = 40241.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  14493  Z= 0.099
  Angle     :  0.619  11.188  19617  Z= 0.303
  Chirality :  0.043   0.178   2130
  Planarity :  0.004   0.061   2512
  Dihedral  :  4.783  45.155   1894
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.83 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.21), residues: 1663
  helix: -0.45 (0.37), residues: 211
  sheet: -0.32 (0.27), residues: 354
  loop : -0.82 (0.20), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 439 
 HIS   0.004   0.000   HIS D   5 
 PHE   0.013   0.001   PHE B 283 
 TYR   0.012   0.001   TYR B 872 
 ARG   0.003   0.000   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02998 (  313)
  hydrogen bonds       : angle       5.78535 (  897)
  SS BOND              : bond        0.00149 (   40)
  SS BOND              : angle       0.63078 (   80)
  covalent geometry    : bond        0.00233 (14453)
  covalent geometry    : angle       0.61893 (19537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5317.56 seconds
wall clock time: 93 minutes 30.89 seconds (5610.89 seconds total)