Starting phenix.real_space_refine
on Fri Jun 13 22:46:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uid_42293/06_2025/8uid_42293.cif"
  }
  resolution = 2.81
  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=  -0.002 sd=   0.276
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      44      5.16       5
     C   10098      2.51       5
     N    2628      2.21       5
     O    2868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15638
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 738, 5968
          Classifications: {'peptide': 738}
          Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 701}
    Chain: "B"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1851
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 14, 'TRANS': 212}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 14.37, per 1000 atoms: 0.92
  Number of scatterers: 15638
  At special positions: 0
  Unit cell: (105.78, 128.14, 86.86, 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      44     16.00
     O    2868      8.00
     N    2628      7.00
     C   10098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.62
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3540

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 28 sheets defined
      20.3% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 16
      No H-bonds generated for 'chain 'A' and resid 14 through 16'
    Processing helix  chain 'A' and resid 17 through 28
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 67 through 78
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS A 106 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.559A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 248 " --> pdb=" O   PRO A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.541A  pdb=" N   SER A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 619 through 625
    Processing helix  chain 'A' and resid 722 through 729
    Processing helix  chain 'A' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS A 735 " --> pdb=" O   GLU A 731 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 807
      removed outlier: 3.524A  pdb=" N   LEU B 807 " --> pdb=" O   THR B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 804 through 807'
    Processing helix  chain 'B' and resid 844 through 849
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 868 through 871
    Processing helix  chain 'C' and resid 14 through 16
      No H-bonds generated for 'chain 'C' and resid 14 through 16'
    Processing helix  chain 'C' and resid 17 through 28
    Processing helix  chain 'C' and resid 38 through 43
    Processing helix  chain 'C' and resid 67 through 78
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS C 106 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS C 119 " --> pdb=" O   PRO C 115 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      Proline residue:  C 134  - end of helix
    Processing helix  chain 'C' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 211
      removed outlier: 3.561A  pdb=" N   PHE C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR C 247 " --> pdb=" O   PRO C 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU C 248 " --> pdb=" O   PRO C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR C 302 " --> pdb=" O   SER C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 320
      removed outlier: 3.542A  pdb=" N   SER C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 598 through 603
    Processing helix  chain 'C' and resid 619 through 625
    Processing helix  chain 'C' and resid 722 through 729
    Processing helix  chain 'C' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS C 735 " --> pdb=" O   GLU C 731 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 804 through 807
      removed outlier: 3.523A  pdb=" N   LEU D 807 " --> pdb=" O   THR D 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 804 through 807'
    Processing helix  chain 'D' and resid 844 through 849
    Processing helix  chain 'D' and resid 850 through 855
    Processing helix  chain 'D' and resid 868 through 871
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175
      removed outlier: 3.788A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A  82 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   GLN A 145 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA A  84 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A  33 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ARG A  85 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   THR A  35 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   LEU A   4 " --> pdb=" O   CYS A  32 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   SER A  34 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLY A   6 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR A  36 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   GLU A   7 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 266 " --> pdb=" O   GLU A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 329
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 340
      removed outlier: 3.879A  pdb=" N   LEU A 385 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL A 398 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 389 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LYS A 396 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA A 429 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR A 400 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU A 427 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359
    Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA A 404 " --> pdb=" O   TYR A 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A 419 " --> pdb=" O   ALA A 404 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 406 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE A 480 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET A 416 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   THR A 482 " --> pdb=" O   MET A 416 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ILE A 418 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 438 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU A 497 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510
      removed outlier: 3.541A  pdb=" N   ALA A 540 " --> pdb=" O   LYS B 971 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ILE A 541 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 574
    Processing sheet with id=AA9, first strand: chain 'A' and resid 573 through 574
      removed outlier: 5.151A  pdb=" N   ILE B 952 " --> pdb=" O   TRP B 900 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TRP B 900 " --> pdb=" O   ILE B 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B 893 " --> pdb=" O   VAL B 927 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR A 579 " --> pdb=" O   ALA B 861 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 914 " --> pdb=" O   VAL B 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL B 908 " --> pdb=" O   PHE B 912 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   PHE B 912 " --> pdb=" O   VAL B 908 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP B 838 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU B 837 " --> pdb=" O   ARG A 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE A 644 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   TYR A 648 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 659
      removed outlier: 6.926A  pdb=" N   PHE A 636 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR A 692 " --> pdb=" O   PHE A 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR B 832 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704
      removed outlier: 3.514A  pdb=" N   GLY A 701 " --> pdb=" O   VAL B 829 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL B 789 " --> pdb=" O   TYR B 793 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TYR B 793 " --> pdb=" O   VAL B 789 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 175
      removed outlier: 3.787A  pdb=" N   LEU C 173 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL C  82 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLN C 145 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA C  84 " --> pdb=" O   GLN C 145 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL C  33 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   ARG C  85 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   THR C  35 " --> pdb=" O   ARG C  85 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   LEU C   4 " --> pdb=" O   CYS C  32 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   SER C  34 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   GLY C   6 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR C  36 " --> pdb=" O   GLY C   6 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   GLU C   7 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET C 266 " --> pdb=" O   GLU C   7 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 329
    Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 340
      removed outlier: 3.880A  pdb=" N   LEU C 385 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL C 398 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL C 389 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LYS C 396 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA C 429 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR C 400 " --> pdb=" O   GLU C 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU C 427 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 357 through 359
    Processing sheet with id=AC1, first strand: chain 'C' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA C 404 " --> pdb=" O   TYR C 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR C 419 " --> pdb=" O   ALA C 404 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU C 406 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL C 414 " --> pdb=" O   LEU C 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE C 480 " --> pdb=" O   VAL C 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET C 416 " --> pdb=" O   ILE C 480 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   THR C 482 " --> pdb=" O   MET C 416 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE C 418 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP C 438 " --> pdb=" O   LYS C 470 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU C 497 " --> pdb=" O   VAL C 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C 557 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 509 through 510
      removed outlier: 3.542A  pdb=" N   ALA C 540 " --> pdb=" O   LYS D 971 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE C 541 " --> pdb=" O   LEU C 548 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 573 through 574
    Processing sheet with id=AC5, first strand: chain 'C' and resid 573 through 574
      removed outlier: 5.150A  pdb=" N   ILE D 952 " --> pdb=" O   TRP D 900 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   TRP D 900 " --> pdb=" O   ILE D 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL D 893 " --> pdb=" O   VAL D 927 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR C 579 " --> pdb=" O   ALA D 861 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY D 914 " --> pdb=" O   VAL D 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL D 908 " --> pdb=" O   PHE D 912 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   PHE D 912 " --> pdb=" O   VAL D 908 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP D 838 " --> pdb=" O   ILE C 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU D 837 " --> pdb=" O   ARG C 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE C 644 " --> pdb=" O   TYR C 648 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   TYR C 648 " --> pdb=" O   ILE C 644 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 655 through 659
      removed outlier: 6.927A  pdb=" N   PHE C 636 " --> pdb=" O   TYR C 692 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   TYR C 692 " --> pdb=" O   PHE C 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR D 832 " --> pdb=" O   LEU C 697 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 701 through 704
      removed outlier: 3.515A  pdb=" N   GLY C 701 " --> pdb=" O   VAL D 829 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL D 789 " --> pdb=" O   TYR D 793 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   TYR D 793 " --> pdb=" O   VAL D 789 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1584 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: 6.92

  Time building geometry restraints manager: 4.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3902
        1.33 -     1.45: 3313
        1.45 -     1.58: 8763
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 16044
  Sorted by residual:
  bond pdb=" CZ  ARG C 111 "
       pdb=" NH2 ARG C 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.284  0.046 1.30e-02 5.92e+03 1.23e+01
  bond pdb=" CA  LYS A 322 "
       pdb=" C   LYS A 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.20e+01
  bond pdb=" CA  LYS C 322 "
       pdb=" C   LYS C 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.18e+01
  bond pdb=" CZ  ARG A 111 "
       pdb=" NH2 ARG A 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" CZ  ARG C 300 "
       pdb=" NH2 ARG C 300 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.16e+01
  ... (remaining 16039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 17838
        2.46 -     4.92: 3660
        4.92 -     7.37: 285
        7.37 -     9.83: 29
        9.83 -    12.29: 2
  Bond angle restraints: 21814
  Sorted by residual:
  angle pdb=" CA  LYS C 322 "
        pdb=" C   LYS C 322 "
        pdb=" N   PRO C 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.08   -5.40 7.10e-01 1.98e+00 5.79e+01
  angle pdb=" CA  LYS A 322 "
        pdb=" C   LYS A 322 "
        pdb=" N   PRO A 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.06   -5.38 7.10e-01 1.98e+00 5.74e+01
  angle pdb=" CA  ARG A 239 "
        pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.82e+01
  angle pdb=" CA  ARG C 239 "
        pdb=" C   ARG C 239 "
        pdb=" N   LEU C 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.81e+01
  angle pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
        pdb=" CA  LEU A 240 "
      ideal   model   delta    sigma   weight residual
     121.70  133.99  -12.29 1.80e+00 3.09e-01 4.66e+01
  ... (remaining 21809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 8309
       15.98 -    31.96: 851
       31.96 -    47.94: 196
       47.94 -    63.92: 70
       63.92 -    79.90: 30
  Dihedral angle restraints: 9456
    sinusoidal: 3866
      harmonic: 5590
  Sorted by residual:
  dihedral pdb=" C   ASP A 638 "
           pdb=" N   ASP A 638 "
           pdb=" CA  ASP A 638 "
           pdb=" CB  ASP A 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.65   17.05     0      2.50e+00 1.60e-01 4.65e+01
  dihedral pdb=" C   ASP C 638 "
           pdb=" N   ASP C 638 "
           pdb=" CA  ASP C 638 "
           pdb=" CB  ASP C 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.62   17.02     0      2.50e+00 1.60e-01 4.63e+01
  dihedral pdb=" CA  ASN C 148 "
           pdb=" C   ASN C 148 "
           pdb=" N   GLU C 149 "
           pdb=" CA  GLU C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.63   29.37     0      5.00e+00 4.00e-02 3.45e+01
  ... (remaining 9453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2017
       0.148 -    0.296: 332
       0.296 -    0.444: 25
       0.444 -    0.592: 4
       0.592 -    0.740: 2
  Chirality restraints: 2380
  Sorted by residual:
  chirality pdb=" CA  ASP A 638 "
            pdb=" N   ASP A 638 "
            pdb=" C   ASP A 638 "
            pdb=" CB  ASP A 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CA  ASP C 638 "
            pdb=" N   ASP C 638 "
            pdb=" C   ASP C 638 "
            pdb=" CB  ASP C 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CB  ILE D 939 "
            pdb=" CA  ILE D 939 "
            pdb=" CG1 ILE D 939 "
            pdb=" CG2 ILE D 939 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.52 2.00e-01 2.50e+01 6.78e+00
  ... (remaining 2377 not shown)

  Planarity restraints: 2780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 196 "    0.182 2.00e-02 2.50e+03   9.21e-02 2.12e+02
        pdb=" CG  TRP C 196 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 196 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 196 "   -0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 196 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 196 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 196 "   -0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 196 "    0.100 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 196 "   -0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 196 "    0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 196 "   -0.182 2.00e-02 2.50e+03   9.20e-02 2.12e+02
        pdb=" CG  TRP A 196 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 196 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 196 "    0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 196 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 196 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 196 "    0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 196 "   -0.099 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 196 "    0.030 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 196 "   -0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  10 "    0.173 2.00e-02 2.50e+03   1.01e-01 2.03e+02
        pdb=" CG  TYR C  10 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  10 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  10 "   -0.084 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  10 "   -0.075 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  10 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  10 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR C  10 "    0.164 2.00e-02 2.50e+03
  ... (remaining 2777 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 10
        2.38 -     3.01: 7893
        3.01 -     3.64: 23349
        3.64 -     4.27: 41477
        4.27 -     4.90: 67466
  Nonbonded interactions: 140195
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 824 "
            pdb=" NH2 ARG C 360 "
     model   vdw
     1.749 3.200
  nonbonded pdb=" NH2 ARG A 360 "
            pdb=" ND2 ASN D 824 "
     model   vdw
     1.785 3.200
  nonbonded pdb=" OG  SER B 749 "
            pdb=" O   ALA C 330 "
     model   vdw
     1.895 3.040
  nonbonded pdb=" O   ALA A 330 "
            pdb=" OG  SER D 749 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" NH2 ARG A 375 "
            pdb=" O   ARG C 231 "
     model   vdw
     2.133 3.120
  ... (remaining 140190 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             91.480
  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:             0.020
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     44.160
  Find NCS groups from input model:        0.300
  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:11.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  148.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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      :  0.013   0.046  16044  Z= 0.764
  Angle     :  1.898  12.291  21814  Z= 1.249
  Chirality :  0.110   0.740   2380
  Planarity :  0.018   0.169   2780
  Dihedral  : 15.024  79.899   5916
  Min Nonbonded Distance : 1.749

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  :  6.82 %
    Favored  : 89.13 %
  Cbeta Deviations :  1.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -1.38 (0.17), residues: 1922
  helix: -1.81 (0.23), residues: 310
  sheet:  0.40 (0.24), residues: 404
  loop : -1.16 (0.17), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.182   0.024   TRP A 196 
 HIS   0.018   0.005   HIS A 460 
 PHE   0.082   0.019   PHE A 310 
 TYR   0.187   0.026   TYR A 235 
 ARG   0.014   0.002   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13956 (  596)
  hydrogen bonds       : angle       7.47140 ( 1584)
  covalent geometry    : bond        0.01261 (16044)
  covalent geometry    : angle       1.89847 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 319
  time to evaluate  : 1.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 SER cc_start: 0.8370 (m) cc_final: 0.7983 (t)
REVERT: A  218 MET cc_start: 0.8503 (ttt) cc_final: 0.8147 (ttp)
REVERT: A  355 ASN cc_start: 0.7681 (m-40) cc_final: 0.7434 (m110)
REVERT: B  840 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8060 (pp)
REVERT: B  885 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7946 (ptmt)
REVERT: C  194 SER cc_start: 0.8380 (m) cc_final: 0.8010 (t)
REVERT: C  218 MET cc_start: 0.8511 (ttt) cc_final: 0.8151 (ttp)
REVERT: C  355 ASN cc_start: 0.7723 (m-40) cc_final: 0.7466 (m110)
REVERT: D  840 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (pp)
REVERT: D  885 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7961 (ptmt)
  outliers start: 69
  outliers final: 12
  residues processed: 375
  average time/residue: 1.5295
  time to fit residues: 626.1031
Evaluate side-chains
  181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 1.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  840 ILE
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  552 ARG
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  840 ILE
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    0.7980
   chunk 144 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 148 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 172 optimal weight:    4.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 145 GLN
A 177 ASN
A 272 ASN
A 460 HIS
C  59 HIS
C 145 GLN
C 177 ASN
C 272 ASN
C 460 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.152025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.127180 restraints weight = 17520.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.81
r_work: 0.3411 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16044  Z= 0.146
  Angle     :  0.679   9.551  21814  Z= 0.365
  Chirality :  0.050   0.221   2380
  Planarity :  0.005   0.048   2780
  Dihedral  :  7.313  58.260   2202
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.39 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.59 (0.19), residues: 1922
  helix: -0.20 (0.28), residues: 304
  sheet:  0.45 (0.24), residues: 472
  loop : -0.81 (0.18), residues: 1146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 152 
 HIS   0.005   0.001   HIS C  59 
 PHE   0.016   0.002   PHE D 788 
 TYR   0.028   0.002   TYR D 832 
 ARG   0.007   0.001   ARG B 934 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04137 (  596)
  hydrogen bonds       : angle       5.74972 ( 1584)
  covalent geometry    : bond        0.00320 (16044)
  covalent geometry    : angle       0.67871 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 217
  time to evaluate  : 1.965 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8184 (t70) cc_final: 0.7751 (m-30)
REVERT: A  168 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7215 (mtpp)
REVERT: A  199 ARG cc_start: 0.7108 (mmp-170) cc_final: 0.6738 (mpp-170)
REVERT: A  218 MET cc_start: 0.9012 (ttt) cc_final: 0.8709 (ttp)
REVERT: A  299 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7439 (tp30)
REVERT: A  338 GLN cc_start: 0.8189 (tt0) cc_final: 0.7863 (pt0)
REVERT: A  355 ASN cc_start: 0.8513 (m-40) cc_final: 0.7681 (p0)
REVERT: A  452 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7417 (mt-10)
REVERT: A  524 GLU cc_start: 0.7709 (pm20) cc_final: 0.6772 (pt0)
REVERT: B  759 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7497 (mm-30)
REVERT: B  859 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7539 (mp0)
REVERT: B  939 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7790 (mt)
REVERT: C   20 ASP cc_start: 0.8208 (t70) cc_final: 0.7762 (m-30)
REVERT: C  168 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7288 (mtpp)
REVERT: C  199 ARG cc_start: 0.7156 (mmp-170) cc_final: 0.6791 (mpp-170)
REVERT: C  218 MET cc_start: 0.9028 (ttt) cc_final: 0.8729 (ttp)
REVERT: C  299 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7416 (tp30)
REVERT: C  338 GLN cc_start: 0.8202 (tt0) cc_final: 0.7891 (pt0)
REVERT: C  355 ASN cc_start: 0.8487 (m-40) cc_final: 0.7596 (p0)
REVERT: C  446 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7661 (mt)
REVERT: C  524 GLU cc_start: 0.7686 (pm20) cc_final: 0.6764 (pt0)
REVERT: D  759 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: D  859 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6390 (mp0)
REVERT: D  939 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7790 (mt)
  outliers start: 68
  outliers final: 17
  residues processed: 262
  average time/residue: 1.4855
  time to fit residues: 428.4932
Evaluate side-chains
  185 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  859 GLU
Chi-restraints excluded: chain B residue  889 SER
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  889 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 117 optimal weight:    7.9990
   chunk 119 optimal weight:    6.9990
   chunk 170 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 149 optimal weight:    8.9990
   chunk 159 optimal weight:    1.9990
   chunk 137 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN
A 312 ASN
C 263 ASN
C 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.144153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.118025 restraints weight = 17525.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.88
r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16044  Z= 0.164
  Angle     :  0.648   9.137  21814  Z= 0.342
  Chirality :  0.050   0.240   2380
  Planarity :  0.005   0.039   2780
  Dihedral  :  6.591  59.415   2188
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 15.63 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.49 (0.19), residues: 1922
  helix:  0.17 (0.29), residues: 304
  sheet:  0.37 (0.24), residues: 476
  loop : -0.75 (0.18), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 152 
 HIS   0.005   0.001   HIS C 460 
 PHE   0.013   0.002   PHE C 216 
 TYR   0.016   0.002   TYR C 639 
 ARG   0.004   0.001   ARG B 948 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  596)
  hydrogen bonds       : angle       5.36502 ( 1584)
  covalent geometry    : bond        0.00378 (16044)
  covalent geometry    : angle       0.64780 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 168
  time to evaluate  : 1.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8156 (t70) cc_final: 0.7656 (m-30)
REVERT: A  108 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6172 (mmt)
REVERT: A  119 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7732 (ptpt)
REVERT: A  135 TYR cc_start: 0.8276 (m-80) cc_final: 0.7635 (m-80)
REVERT: A  199 ARG cc_start: 0.6985 (mmp-170) cc_final: 0.6577 (tpp80)
REVERT: A  299 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7235 (tp30)
REVERT: A  325 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5868 (mp0)
REVERT: A  338 GLN cc_start: 0.8030 (tt0) cc_final: 0.7705 (pt0)
REVERT: A  355 ASN cc_start: 0.8564 (m-40) cc_final: 0.7646 (p0)
REVERT: A  446 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7573 (mt)
REVERT: A  452 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7370 (mt-10)
REVERT: A  524 GLU cc_start: 0.7704 (pm20) cc_final: 0.7287 (mp0)
REVERT: A  539 GLU cc_start: 0.7624 (tp30) cc_final: 0.7378 (mt-10)
REVERT: A  662 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7754 (m)
REVERT: A  675 GLU cc_start: 0.8468 (tt0) cc_final: 0.8158 (tt0)
REVERT: B  759 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7632 (mm-30)
REVERT: B  808 LYS cc_start: 0.8136 (pttp) cc_final: 0.7916 (pptt)
REVERT: B  939 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7765 (mt)
REVERT: C   20 ASP cc_start: 0.8127 (t70) cc_final: 0.7639 (m-30)
REVERT: C  119 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7758 (ptpt)
REVERT: C  135 TYR cc_start: 0.8240 (m-80) cc_final: 0.7633 (m-80)
REVERT: C  199 ARG cc_start: 0.7012 (mmp-170) cc_final: 0.6568 (tpp80)
REVERT: C  299 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7230 (tp30)
REVERT: C  325 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5905 (mp0)
REVERT: C  338 GLN cc_start: 0.8068 (tt0) cc_final: 0.7759 (pt0)
REVERT: C  446 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: C  494 ASP cc_start: 0.6975 (t0) cc_final: 0.6658 (t0)
REVERT: C  524 GLU cc_start: 0.7595 (pm20) cc_final: 0.7177 (mp0)
REVERT: C  539 GLU cc_start: 0.7580 (tp30) cc_final: 0.7321 (mt-10)
REVERT: C  568 ARG cc_start: 0.5572 (mmt-90) cc_final: 0.5359 (mmt-90)
REVERT: D  759 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7472 (mm-30)
REVERT: D  808 LYS cc_start: 0.8152 (pttp) cc_final: 0.7933 (pptt)
REVERT: D  859 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6348 (mp0)
REVERT: D  939 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7796 (mt)
  outliers start: 79
  outliers final: 20
  residues processed: 225
  average time/residue: 1.6016
  time to fit residues: 394.6809
Evaluate side-chains
  175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 2.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 184 optimal weight:    0.4980
   chunk 124 optimal weight:    4.9990
   chunk 138 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 187 optimal weight:    0.7980
   chunk 159 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 422 HIS
A 476 ASN
C 422 HIS
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 476 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115011 restraints weight = 17633.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.91
r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16044  Z= 0.204
  Angle     :  0.657   9.132  21814  Z= 0.344
  Chirality :  0.050   0.260   2380
  Planarity :  0.005   0.043   2780
  Dihedral  :  6.532  59.195   2188
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 17.27 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.51 (0.19), residues: 1922
  helix:  0.23 (0.29), residues: 304
  sheet:  0.21 (0.24), residues: 486
  loop : -0.72 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 152 
 HIS   0.005   0.001   HIS A 460 
 PHE   0.011   0.002   PHE C 216 
 TYR   0.015   0.002   TYR A 135 
 ARG   0.004   0.001   ARG B 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  596)
  hydrogen bonds       : angle       5.31773 ( 1584)
  covalent geometry    : bond        0.00481 (16044)
  covalent geometry    : angle       0.65696 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 165
  time to evaluate  : 1.750 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8129 (t70) cc_final: 0.7643 (m-30)
REVERT: A   77 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6853 (tp30)
REVERT: A  108 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6181 (mmt)
REVERT: A  119 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7790 (ptpt)
REVERT: A  199 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.6599 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7286 (tp30)
REVERT: A  325 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5797 (mp0)
REVERT: A  338 GLN cc_start: 0.8108 (tt0) cc_final: 0.7717 (pt0)
REVERT: A  355 ASN cc_start: 0.8566 (m-40) cc_final: 0.8272 (m-40)
REVERT: A  446 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7578 (mt)
REVERT: A  452 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7347 (mt-10)
REVERT: A  494 ASP cc_start: 0.7069 (t0) cc_final: 0.6714 (t0)
REVERT: A  524 GLU cc_start: 0.7562 (pm20) cc_final: 0.7237 (mp0)
REVERT: A  539 GLU cc_start: 0.7647 (tp30) cc_final: 0.7387 (mp0)
REVERT: A  583 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7004 (tp30)
REVERT: A  675 GLU cc_start: 0.8409 (tt0) cc_final: 0.8207 (tt0)
REVERT: B  759 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7677 (mm-30)
REVERT: B  819 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (mp0)
REVERT: B  859 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6388 (mp0)
REVERT: C   20 ASP cc_start: 0.8132 (t70) cc_final: 0.7643 (m-30)
REVERT: C   77 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6869 (tp30)
REVERT: C  108 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6313 (mmt)
REVERT: C  119 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7776 (ptpt)
REVERT: C  199 ARG cc_start: 0.7127 (mmp-170) cc_final: 0.6595 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7278 (tp30)
REVERT: C  325 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5779 (mp0)
REVERT: C  338 GLN cc_start: 0.8127 (tt0) cc_final: 0.7828 (pt0)
REVERT: C  355 ASN cc_start: 0.8597 (m-40) cc_final: 0.8276 (m-40)
REVERT: C  446 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: C  494 ASP cc_start: 0.7027 (t0) cc_final: 0.6628 (t0)
REVERT: C  524 GLU cc_start: 0.7520 (pm20) cc_final: 0.7210 (mp0)
REVERT: C  539 GLU cc_start: 0.7665 (tp30) cc_final: 0.7452 (mt-10)
REVERT: D  759 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7494 (mm-30)
  outliers start: 83
  outliers final: 32
  residues processed: 225
  average time/residue: 1.4933
  time to fit residues: 372.3369
Evaluate side-chains
  195 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 151
  time to evaluate  : 1.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  819 GLU
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  535 SER
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 122 optimal weight:    0.5980
   chunk 166 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 180 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.144897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.118806 restraints weight = 17796.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.92
r_work: 0.3291 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16044  Z= 0.133
  Angle     :  0.582   8.590  21814  Z= 0.307
  Chirality :  0.048   0.254   2380
  Planarity :  0.004   0.048   2780
  Dihedral  :  5.987  58.091   2184
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.16 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.39 (0.19), residues: 1922
  helix:  0.55 (0.30), residues: 304
  sheet:  0.36 (0.24), residues: 458
  loop : -0.72 (0.19), residues: 1160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 152 
 HIS   0.002   0.001   HIS A 588 
 PHE   0.013   0.001   PHE B 788 
 TYR   0.013   0.001   TYR A 639 
 ARG   0.005   0.000   ARG D 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  596)
  hydrogen bonds       : angle       5.21228 ( 1584)
  covalent geometry    : bond        0.00303 (16044)
  covalent geometry    : angle       0.58180 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 164
  time to evaluate  : 1.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7967 (t70) cc_final: 0.7525 (m-30)
REVERT: A   73 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7506 (mt-10)
REVERT: A   77 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6834 (tp30)
REVERT: A  108 MET cc_start: 0.7530 (mpp) cc_final: 0.6166 (mmt)
REVERT: A  135 TYR cc_start: 0.8294 (m-80) cc_final: 0.7672 (m-80)
REVERT: A  199 ARG cc_start: 0.7109 (mmp-170) cc_final: 0.6625 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7177 (tp30)
REVERT: A  325 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5732 (mp0)
REVERT: A  338 GLN cc_start: 0.8013 (tt0) cc_final: 0.7805 (pt0)
REVERT: A  355 ASN cc_start: 0.8499 (m-40) cc_final: 0.7596 (p0)
REVERT: A  446 LEU cc_start: 0.8417 (tt) cc_final: 0.7518 (mt)
REVERT: A  452 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7347 (mt-10)
REVERT: A  494 ASP cc_start: 0.7190 (t0) cc_final: 0.6817 (t0)
REVERT: A  524 GLU cc_start: 0.7578 (pm20) cc_final: 0.7252 (mp0)
REVERT: B  759 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7586 (mm-30)
REVERT: B  808 LYS cc_start: 0.8110 (pttp) cc_final: 0.7853 (pptt)
REVERT: B  813 GLU cc_start: 0.8199 (tt0) cc_final: 0.7958 (tt0)
REVERT: B  859 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6364 (mp0)
REVERT: C   20 ASP cc_start: 0.7985 (t70) cc_final: 0.7530 (m-30)
REVERT: C   77 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6807 (tp30)
REVERT: C  108 MET cc_start: 0.7660 (mpp) cc_final: 0.6349 (mmt)
REVERT: C  119 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7642 (mtpt)
REVERT: C  135 TYR cc_start: 0.8288 (m-80) cc_final: 0.7633 (m-80)
REVERT: C  199 ARG cc_start: 0.7132 (mmp-170) cc_final: 0.6623 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7164 (tp30)
REVERT: C  325 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5690 (mp0)
REVERT: C  446 LEU cc_start: 0.8438 (tt) cc_final: 0.7532 (mt)
REVERT: C  494 ASP cc_start: 0.7158 (t0) cc_final: 0.6799 (t0)
REVERT: C  524 GLU cc_start: 0.7430 (pm20) cc_final: 0.7188 (mp0)
REVERT: C  583 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7542 (tt0)
REVERT: D  808 LYS cc_start: 0.8130 (pttp) cc_final: 0.7866 (pptt)
REVERT: D  859 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6297 (mp0)
REVERT: D  948 ARG cc_start: 0.8351 (mmt90) cc_final: 0.8140 (mmt180)
  outliers start: 74
  outliers final: 25
  residues processed: 226
  average time/residue: 1.3856
  time to fit residues: 345.0103
Evaluate side-chains
  175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0370
   chunk 82 optimal weight:    4.9990
   chunk 138 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    2.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
C 145 GLN
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113235 restraints weight = 17806.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.92
r_work: 0.3211 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  16044  Z= 0.237
  Angle     :  0.669   9.175  21814  Z= 0.349
  Chirality :  0.050   0.237   2380
  Planarity :  0.005   0.043   2780
  Dihedral  :  6.317  59.320   2184
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.45 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.64 (0.19), residues: 1922
  helix:  0.34 (0.30), residues: 306
  sheet: -0.07 (0.23), residues: 478
  loop : -0.78 (0.19), residues: 1138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 152 
 HIS   0.005   0.001   HIS A 460 
 PHE   0.011   0.002   PHE A 310 
 TYR   0.015   0.002   TYR C 135 
 ARG   0.005   0.001   ARG A 615 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  596)
  hydrogen bonds       : angle       5.32952 ( 1584)
  covalent geometry    : bond        0.00569 (16044)
  covalent geometry    : angle       0.66890 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 146
  time to evaluate  : 1.739 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8105 (t70) cc_final: 0.7622 (m-30)
REVERT: A   77 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6874 (tp30)
REVERT: A   85 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7707 (mtp85)
REVERT: A  108 MET cc_start: 0.7580 (mpp) cc_final: 0.6234 (mmt)
REVERT: A  299 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7293 (tp30)
REVERT: A  325 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5677 (mp0)
REVERT: A  338 GLN cc_start: 0.8169 (tt0) cc_final: 0.7823 (pt0)
REVERT: A  355 ASN cc_start: 0.8615 (m-40) cc_final: 0.8177 (m-40)
REVERT: A  446 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7561 (mt)
REVERT: A  452 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7364 (mt-10)
REVERT: A  494 ASP cc_start: 0.7256 (t0) cc_final: 0.6875 (t0)
REVERT: A  524 GLU cc_start: 0.7533 (pm20) cc_final: 0.7207 (mp0)
REVERT: A  539 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7543 (mp0)
REVERT: A  583 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7056 (tp30)
REVERT: B  759 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7704 (mm-30)
REVERT: B  859 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6395 (mp0)
REVERT: C   20 ASP cc_start: 0.8121 (t70) cc_final: 0.7629 (m-30)
REVERT: C   77 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6864 (tp30)
REVERT: C  108 MET cc_start: 0.7619 (mpp) cc_final: 0.6342 (mmt)
REVERT: C  119 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7804 (ptpt)
REVERT: C  299 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7284 (tp30)
REVERT: C  325 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5865 (mp0)
REVERT: C  355 ASN cc_start: 0.8698 (m-40) cc_final: 0.8375 (m-40)
REVERT: C  446 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7587 (mt)
REVERT: C  494 ASP cc_start: 0.7231 (t0) cc_final: 0.6836 (t0)
REVERT: C  524 GLU cc_start: 0.7484 (pm20) cc_final: 0.7194 (mp0)
REVERT: C  539 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7512 (mp0)
REVERT: C  735 LYS cc_start: 0.7030 (mmtp) cc_final: 0.6035 (mptm)
REVERT: D  759 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7468 (mm-30)
REVERT: D  859 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6373 (mp0)
  outliers start: 78
  outliers final: 31
  residues processed: 206
  average time/residue: 1.3444
  time to fit residues: 306.5061
Evaluate side-chains
  179 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 179 optimal weight:    0.0060
   chunk 73 optimal weight:   10.0000
   chunk 155 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9980
   chunk 163 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   chunk 135 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9980
   chunk 173 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
A 588 HIS
C 145 GLN
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.144700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.118565 restraints weight = 17640.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.91
r_work: 0.3288 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16044  Z= 0.119
  Angle     :  0.567   8.479  21814  Z= 0.299
  Chirality :  0.047   0.276   2380
  Planarity :  0.004   0.047   2780
  Dihedral  :  5.905  57.773   2184
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.15 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.47 (0.19), residues: 1922
  helix:  0.65 (0.30), residues: 306
  sheet:  0.13 (0.23), residues: 472
  loop : -0.76 (0.19), residues: 1144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 588 
 PHE   0.015   0.001   PHE A 587 
 TYR   0.014   0.001   TYR A 639 
 ARG   0.005   0.000   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  596)
  hydrogen bonds       : angle       5.17608 ( 1584)
  covalent geometry    : bond        0.00266 (16044)
  covalent geometry    : angle       0.56672 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 153
  time to evaluate  : 1.804 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7961 (t70) cc_final: 0.7526 (m-30)
REVERT: A   77 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6833 (tp30)
REVERT: A   85 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7530 (mtp85)
REVERT: A  108 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6254 (mmt)
REVERT: A  135 TYR cc_start: 0.8324 (m-80) cc_final: 0.7750 (m-80)
REVERT: A  199 ARG cc_start: 0.7331 (tpm-80) cc_final: 0.6720 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7174 (tp30)
REVERT: A  316 GLU cc_start: 0.7918 (tt0) cc_final: 0.7603 (pm20)
REVERT: A  325 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5745 (mp0)
REVERT: A  446 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7590 (mt)
REVERT: A  447 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7451 (mp)
REVERT: A  452 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7307 (mt-10)
REVERT: A  494 ASP cc_start: 0.7324 (t0) cc_final: 0.6917 (t0)
REVERT: A  524 GLU cc_start: 0.7537 (pm20) cc_final: 0.7260 (mp0)
REVERT: A  539 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7445 (mp0)
REVERT: A  615 ARG cc_start: 0.7226 (mtt-85) cc_final: 0.6954 (mmt-90)
REVERT: A  735 LYS cc_start: 0.6880 (mmtp) cc_final: 0.5986 (mptt)
REVERT: B  759 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7613 (mm-30)
REVERT: B  808 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7840 (pptt)
REVERT: B  813 GLU cc_start: 0.8179 (tt0) cc_final: 0.7917 (tt0)
REVERT: B  859 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6387 (mp0)
REVERT: C   20 ASP cc_start: 0.7984 (t70) cc_final: 0.7542 (m-30)
REVERT: C   77 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6806 (tp30)
REVERT: C  108 MET cc_start: 0.7605 (mpp) cc_final: 0.6319 (mmt)
REVERT: C  135 TYR cc_start: 0.8305 (m-80) cc_final: 0.7689 (m-80)
REVERT: C  199 ARG cc_start: 0.7326 (tpm-80) cc_final: 0.6711 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7161 (tp30)
REVERT: C  446 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7555 (mt)
REVERT: C  494 ASP cc_start: 0.7310 (t0) cc_final: 0.6867 (t0)
REVERT: C  524 GLU cc_start: 0.7480 (pm20) cc_final: 0.7237 (mp0)
REVERT: C  539 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7431 (mp0)
REVERT: C  555 LYS cc_start: 0.8623 (tttm) cc_final: 0.8314 (tttm)
REVERT: C  735 LYS cc_start: 0.6872 (mmtp) cc_final: 0.5912 (mptm)
REVERT: D  759 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7310 (mm-30)
REVERT: D  808 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7864 (pptt)
REVERT: D  859 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6329 (mp0)
  outliers start: 71
  outliers final: 25
  residues processed: 210
  average time/residue: 1.4199
  time to fit residues: 330.7621
Evaluate side-chains
  173 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  808 LYS
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  456 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  808 LYS
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 180 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 141 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9980
   chunk 128 optimal weight:    0.4980
   chunk 138 optimal weight:    4.9990
   chunk 160 optimal weight:    2.9990
   chunk 150 optimal weight:    0.8980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
B 831 GLN
C 145 GLN
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119545 restraints weight = 17661.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.85
r_work: 0.3306 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16044  Z= 0.142
  Angle     :  0.580   8.541  21814  Z= 0.305
  Chirality :  0.047   0.245   2380
  Planarity :  0.004   0.038   2780
  Dihedral  :  5.907  58.375   2184
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.27 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.45 (0.19), residues: 1922
  helix:  0.70 (0.30), residues: 306
  sheet:  0.27 (0.23), residues: 460
  loop : -0.81 (0.19), residues: 1156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 152 
 HIS   0.003   0.001   HIS A 460 
 PHE   0.015   0.001   PHE A 587 
 TYR   0.014   0.001   TYR A 639 
 ARG   0.007   0.000   ARG B 934 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  596)
  hydrogen bonds       : angle       5.11625 ( 1584)
  covalent geometry    : bond        0.00328 (16044)
  covalent geometry    : angle       0.58032 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 152
  time to evaluate  : 2.055 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7973 (t70) cc_final: 0.7573 (m-30)
REVERT: A   77 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6970 (tp30)
REVERT: A  108 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6257 (mmt)
REVERT: A  135 TYR cc_start: 0.8327 (m-80) cc_final: 0.7728 (m-80)
REVERT: A  199 ARG cc_start: 0.7437 (tpm-80) cc_final: 0.6773 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7217 (tp30)
REVERT: A  316 GLU cc_start: 0.7935 (tt0) cc_final: 0.7628 (pm20)
REVERT: A  446 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7624 (mt)
REVERT: A  447 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7517 (mp)
REVERT: A  452 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: A  494 ASP cc_start: 0.7364 (t0) cc_final: 0.6975 (t0)
REVERT: A  524 GLU cc_start: 0.7511 (pm20) cc_final: 0.7206 (mp0)
REVERT: A  539 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7412 (mp0)
REVERT: A  555 LYS cc_start: 0.8668 (tttm) cc_final: 0.8358 (tttm)
REVERT: A  735 LYS cc_start: 0.6806 (mmtp) cc_final: 0.5873 (mptm)
REVERT: B  759 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7636 (mm-30)
REVERT: B  813 GLU cc_start: 0.8225 (tt0) cc_final: 0.7970 (tt0)
REVERT: B  859 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6420 (mp0)
REVERT: C   20 ASP cc_start: 0.7983 (t70) cc_final: 0.7588 (m-30)
REVERT: C   77 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6974 (tp30)
REVERT: C  105 THR cc_start: 0.8608 (p) cc_final: 0.8247 (t)
REVERT: C  108 MET cc_start: 0.7611 (mpp) cc_final: 0.6302 (mmt)
REVERT: C  135 TYR cc_start: 0.8338 (m-80) cc_final: 0.7764 (m-80)
REVERT: C  199 ARG cc_start: 0.7430 (tpm-80) cc_final: 0.6771 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7208 (tp30)
REVERT: C  316 GLU cc_start: 0.7962 (tt0) cc_final: 0.7638 (pm20)
REVERT: C  446 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7609 (mt)
REVERT: C  494 ASP cc_start: 0.7349 (t0) cc_final: 0.6881 (t0)
REVERT: C  524 GLU cc_start: 0.7412 (pm20) cc_final: 0.7156 (mp0)
REVERT: C  539 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7525 (mp0)
REVERT: C  583 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7561 (tt0)
REVERT: C  735 LYS cc_start: 0.6769 (mmtp) cc_final: 0.5827 (mptm)
REVERT: D  759 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7463 (mm-30)
REVERT: D  808 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7923 (pptt)
REVERT: D  859 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6337 (mp0)
  outliers start: 60
  outliers final: 28
  residues processed: 195
  average time/residue: 1.5800
  time to fit residues: 342.8155
Evaluate side-chains
  175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 1.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  808 LYS
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 63 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 148 optimal weight:    2.9990
   chunk 132 optimal weight:    0.0050
   chunk 156 optimal weight:    0.9990
   chunk 162 optimal weight:    3.9990
   overall best weight:    1.5800

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 831 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.144297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119078 restraints weight = 17574.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.81
r_work: 0.3295 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16044  Z= 0.160
  Angle     :  0.598   8.711  21814  Z= 0.314
  Chirality :  0.048   0.233   2380
  Planarity :  0.005   0.049   2780
  Dihedral  :  5.973  58.692   2184
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.56 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.52 (0.19), residues: 1922
  helix:  0.66 (0.30), residues: 306
  sheet:  0.21 (0.24), residues: 436
  loop : -0.84 (0.18), residues: 1180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 152 
 HIS   0.003   0.001   HIS A 460 
 PHE   0.019   0.002   PHE A 587 
 TYR   0.014   0.002   TYR A 639 
 ARG   0.010   0.000   ARG C 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  596)
  hydrogen bonds       : angle       5.13338 ( 1584)
  covalent geometry    : bond        0.00375 (16044)
  covalent geometry    : angle       0.59850 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 145
  time to evaluate  : 1.761 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7949 (t70) cc_final: 0.7572 (m-30)
REVERT: A   77 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7000 (tp30)
REVERT: A   85 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7861 (mtp85)
REVERT: A  108 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6315 (mmt)
REVERT: A  199 ARG cc_start: 0.7470 (tpm-80) cc_final: 0.6838 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7298 (tp30)
REVERT: A  316 GLU cc_start: 0.7978 (tt0) cc_final: 0.7657 (pm20)
REVERT: A  446 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7673 (mt)
REVERT: A  447 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7649 (mp)
REVERT: A  452 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7348 (mt-10)
REVERT: A  494 ASP cc_start: 0.7346 (t0) cc_final: 0.6996 (t0)
REVERT: A  524 GLU cc_start: 0.7479 (pm20) cc_final: 0.7241 (mp0)
REVERT: A  539 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7434 (mp0)
REVERT: A  555 LYS cc_start: 0.8683 (tttm) cc_final: 0.8376 (tttm)
REVERT: A  735 LYS cc_start: 0.6818 (mmtp) cc_final: 0.5902 (mptm)
REVERT: B  808 LYS cc_start: 0.8101 (pttp) cc_final: 0.7879 (pptt)
REVERT: B  813 GLU cc_start: 0.8242 (tt0) cc_final: 0.7732 (pp20)
REVERT: B  859 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6477 (mp0)
REVERT: B  873 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7439 (mtm-85)
REVERT: C   20 ASP cc_start: 0.7959 (t70) cc_final: 0.7585 (m-30)
REVERT: C   77 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6980 (tp30)
REVERT: C  105 THR cc_start: 0.8590 (p) cc_final: 0.8252 (t)
REVERT: C  108 MET cc_start: 0.7622 (mpp) cc_final: 0.6334 (mmt)
REVERT: C  135 TYR cc_start: 0.8352 (m-80) cc_final: 0.7778 (m-80)
REVERT: C  199 ARG cc_start: 0.7469 (tpm-80) cc_final: 0.6833 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7276 (tp30)
REVERT: C  316 GLU cc_start: 0.7993 (tt0) cc_final: 0.7708 (pm20)
REVERT: C  446 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7641 (mt)
REVERT: C  494 ASP cc_start: 0.7417 (t0) cc_final: 0.6970 (t0)
REVERT: C  524 GLU cc_start: 0.7438 (pm20) cc_final: 0.7155 (mp0)
REVERT: C  555 LYS cc_start: 0.8654 (tttm) cc_final: 0.8331 (tttm)
REVERT: C  583 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7690 (tt0)
REVERT: C  735 LYS cc_start: 0.6775 (mmtp) cc_final: 0.5872 (mptm)
REVERT: D  759 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7426 (mm-30)
REVERT: D  859 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6445 (mp0)
  outliers start: 59
  outliers final: 33
  residues processed: 188
  average time/residue: 1.4029
  time to fit residues: 291.2324
Evaluate side-chains
  179 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 136
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  873 ARG
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 181 optimal weight:    0.9990
   chunk 157 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 143 optimal weight:    0.9980
   chunk 182 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.145907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120083 restraints weight = 17781.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.91
r_work: 0.3296 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16044  Z= 0.138
  Angle     :  0.580   8.292  21814  Z= 0.304
  Chirality :  0.047   0.222   2380
  Planarity :  0.004   0.044   2780
  Dihedral  :  5.891  59.167   2184
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 21.21 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.48 (0.19), residues: 1922
  helix:  0.78 (0.30), residues: 304
  sheet:  0.24 (0.23), residues: 456
  loop : -0.86 (0.19), residues: 1162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 152 
 HIS   0.003   0.001   HIS A 588 
 PHE   0.019   0.001   PHE A 587 
 TYR   0.019   0.001   TYR D 832 
 ARG   0.009   0.000   ARG C 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  596)
  hydrogen bonds       : angle       5.07415 ( 1584)
  covalent geometry    : bond        0.00319 (16044)
  covalent geometry    : angle       0.58045 (21814)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 138
  time to evaluate  : 1.817 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7968 (t70) cc_final: 0.7513 (m-30)
REVERT: A   77 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6997 (tp30)
REVERT: A  108 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6271 (mmt)
REVERT: A  135 TYR cc_start: 0.8333 (m-80) cc_final: 0.7721 (m-80)
REVERT: A  199 ARG cc_start: 0.7372 (tpm-80) cc_final: 0.6704 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7162 (tp30)
REVERT: A  316 GLU cc_start: 0.7872 (tt0) cc_final: 0.7575 (pm20)
REVERT: A  412 ASP cc_start: 0.7455 (p0) cc_final: 0.6232 (m-30)
REVERT: A  446 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7552 (mt)
REVERT: A  447 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7589 (mp)
REVERT: A  452 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7363 (mt-10)
REVERT: A  494 ASP cc_start: 0.7334 (t0) cc_final: 0.6966 (t0)
REVERT: A  524 GLU cc_start: 0.7477 (pm20) cc_final: 0.7232 (mp0)
REVERT: A  539 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7387 (mp0)
REVERT: A  555 LYS cc_start: 0.8663 (tttm) cc_final: 0.8330 (tttm)
REVERT: A  735 LYS cc_start: 0.6687 (mmtp) cc_final: 0.5804 (mptm)
REVERT: B  808 LYS cc_start: 0.8045 (pttp) cc_final: 0.7731 (pptt)
REVERT: B  813 GLU cc_start: 0.8201 (tt0) cc_final: 0.7609 (pp20)
REVERT: B  859 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6452 (mp0)
REVERT: B  873 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7409 (mtm-85)
REVERT: C   20 ASP cc_start: 0.7972 (t70) cc_final: 0.7520 (m-30)
REVERT: C   77 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6999 (tp30)
REVERT: C  105 THR cc_start: 0.8531 (p) cc_final: 0.8199 (t)
REVERT: C  108 MET cc_start: 0.7667 (mpp) cc_final: 0.6330 (mmt)
REVERT: C  135 TYR cc_start: 0.8315 (m-80) cc_final: 0.7739 (m-80)
REVERT: C  199 ARG cc_start: 0.7375 (tpm-80) cc_final: 0.6700 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7154 (tp30)
REVERT: C  446 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: C  452 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7111 (tt0)
REVERT: C  494 ASP cc_start: 0.7380 (t0) cc_final: 0.6933 (t0)
REVERT: C  524 GLU cc_start: 0.7468 (pm20) cc_final: 0.7119 (mp0)
REVERT: C  555 LYS cc_start: 0.8664 (tttm) cc_final: 0.8335 (tttm)
REVERT: C  583 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7690 (tt0)
REVERT: C  735 LYS cc_start: 0.6684 (mmtp) cc_final: 0.5783 (mptm)
REVERT: D  759 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7364 (mm-30)
REVERT: D  808 LYS cc_start: 0.8082 (pttp) cc_final: 0.7800 (pptt)
REVERT: D  859 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6473 (mp0)
  outliers start: 50
  outliers final: 33
  residues processed: 176
  average time/residue: 1.3851
  time to fit residues: 270.4980
Evaluate side-chains
  174 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  873 ARG
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 181 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 117 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 130 optimal weight:    8.9990
   chunk 111 optimal weight:    0.7980
   chunk 160 optimal weight:    5.9990
   chunk 147 optimal weight:    7.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 588 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115188 restraints weight = 17774.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.87
r_work: 0.3241 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  16044  Z= 0.245
  Angle     :  0.674   8.960  21814  Z= 0.351
  Chirality :  0.051   0.227   2380
  Planarity :  0.005   0.052   2780
  Dihedral  :  6.265  59.980   2184
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.39 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -0.70 (0.19), residues: 1922
  helix:  0.46 (0.30), residues: 306
  sheet:  0.06 (0.23), residues: 458
  loop : -0.95 (0.18), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 152 
 HIS   0.005   0.001   HIS A 460 
 PHE   0.028   0.002   PHE C 587 
 TYR   0.016   0.002   TYR C 234 
 ARG   0.010   0.001   ARG C 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  596)
  hydrogen bonds       : angle       5.27145 ( 1584)
  covalent geometry    : bond        0.00584 (16044)
  covalent geometry    : angle       0.67444 (21814)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12045.42 seconds
wall clock time: 210 minutes 10.75 seconds (12610.75 seconds total)