Starting phenix.real_space_refine
on Wed Jul 30 21:16:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2025/7x05_32917.cif"
  }
  resolution = 3.9
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       4      5.49       5
     S      72      5.16       5
     C    8420      2.51       5
     N    2156      2.21       5
     O    2346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13000
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 801, 6431
          Classifications: {'peptide': 801}
          Link IDs: {'PTRANS': 30, 'TRANS': 770}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 43
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 14.10, per 1000 atoms: 1.08
  Number of scatterers: 13000
  At special positions: 0
  Unit cell: (118.77, 114.49, 127.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      72     16.00
     P       4     15.00
     O    2346      8.00
     N    2156      7.00
     C    8420      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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " NAG C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " NAG D   3 "
  Time building additional restraints: 3.43
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 6 sheets defined
      66.3% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 4.374A  pdb=" N   SER A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 110
    Processing helix  chain 'A' and resid 113 through 132
      removed outlier: 4.347A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 4.433A  pdb=" N   SER A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 227
    Processing helix  chain 'A' and resid 242 through 263
      removed outlier: 3.875A  pdb=" N   LEU A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 282
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 357 through 374
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.888A  pdb=" N   HIS A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 447
      removed outlier: 4.233A  pdb=" N   SER A 427 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.755A  pdb=" N   ASN A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.524A  pdb=" N   LEU A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 490
    Processing helix  chain 'A' and resid 494 through 505
      removed outlier: 3.644A  pdb=" N   ILE A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 504 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 554
      removed outlier: 3.574A  pdb=" N   LEU A 532 " --> pdb=" O   ASP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 564 through 587
      removed outlier: 3.710A  pdb=" N   PHE A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 605
    Processing helix  chain 'A' and resid 619 through 647
      removed outlier: 4.079A  pdb=" N   ASP A 623 " --> pdb=" O   GLN A 619 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 681
    Processing helix  chain 'A' and resid 684 through 706
      removed outlier: 5.329A  pdb=" N   VAL A 697 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   TYR A 698 " --> pdb=" O   THR A 694 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 5.051A  pdb=" N   THR A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   HIS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 720 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
    Processing helix  chain 'A' and resid 764 through 819
    Processing helix  chain 'A' and resid 820 through 857
      Proline residue:  A 826  - end of helix
      removed outlier: 4.998A  pdb=" N   GLY A 854 " --> pdb=" O   ILE A 850 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   LEU A 855 " --> pdb=" O   HIS A 851 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 74
    Processing helix  chain 'B' and resid 76 through 89
      removed outlier: 4.374A  pdb=" N   SER B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 110
    Processing helix  chain 'B' and resid 113 through 132
      removed outlier: 4.349A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 162
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 210 through 215
      removed outlier: 4.434A  pdb=" N   SER B 215 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 227
    Processing helix  chain 'B' and resid 242 through 263
      removed outlier: 3.874A  pdb=" N   LEU B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN B 263 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 311 through 319
    Processing helix  chain 'B' and resid 357 through 374
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.888A  pdb=" N   HIS B 394 " --> pdb=" O   SER B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 447
      removed outlier: 4.231A  pdb=" N   SER B 427 " --> pdb=" O   ASN B 423 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 474
    Processing helix  chain 'B' and resid 474 through 479
      removed outlier: 3.756A  pdb=" N   ASN B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.524A  pdb=" N   LEU B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 490
    Processing helix  chain 'B' and resid 494 through 505
      removed outlier: 3.644A  pdb=" N   ILE B 498 " --> pdb=" O   ALA B 494 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL B 504 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 554
      removed outlier: 3.574A  pdb=" N   LEU B 532 " --> pdb=" O   ASP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 564 through 587
      removed outlier: 3.710A  pdb=" N   PHE B 587 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 605
    Processing helix  chain 'B' and resid 619 through 647
      removed outlier: 4.079A  pdb=" N   ASP B 623 " --> pdb=" O   GLN B 619 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 681
    Processing helix  chain 'B' and resid 684 through 706
      removed outlier: 5.329A  pdb=" N   VAL B 697 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   TYR B 698 " --> pdb=" O   THR B 694 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   PHE B 699 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 720
      removed outlier: 5.051A  pdb=" N   THR B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   HIS B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA B 720 " --> pdb=" O   THR B 716 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 736
    Processing helix  chain 'B' and resid 764 through 819
    Processing helix  chain 'B' and resid 820 through 857
      Proline residue:  B 826  - end of helix
      removed outlier: 4.998A  pdb=" N   GLY B 854 " --> pdb=" O   ILE B 850 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   LEU B 855 " --> pdb=" O   HIS B 851 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 6.268A  pdb=" N   HIS B 175 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ARG B 200 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   THR B 332 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS B 326 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL B 284 " --> pdb=" O   GLN B 346 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   VAL B 348 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL B 286 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ALA B 350 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE B 288 " --> pdb=" O   ALA B 350 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LYS B 352 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 232 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   CYS B 287 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE B 234 " --> pdb=" O   CYS B 287 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   VAL B 289 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE B 236 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   MET B 233 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   MET B 381 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   CYS B 235 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ARG B 461 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   GLY B 406 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE B 405 " --> pdb=" O   THR B 512 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   HIS B 514 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   GLY B 407 " --> pdb=" O   HIS B 514 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515
      removed outlier: 4.205A  pdb=" N   ILE A 405 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   HIS A 514 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   GLY A 407 " --> pdb=" O   HIS A 514 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   GLY A 406 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ARG A 461 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   MET A 233 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   MET A 381 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   CYS A 235 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU A 232 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A 234 " --> pdb=" O   CYS A 287 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   VAL A 289 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE A 236 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL A 284 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
      removed outlier: 8.375A  pdb=" N   VAL A 348 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL A 286 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ALA A 350 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ILE A 288 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LYS A 352 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS A 326 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   THR A 332 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ARG A 200 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   HIS A 175 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL A 174 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   SER B  55 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LYS A 176 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414
      removed outlier: 6.754A  pdb=" N   THR A 413 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 337
    Processing sheet with id=AA6, first strand: chain 'B' and resid 412 through 414
      removed outlier: 6.754A  pdb=" N   THR B 413 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    816 hydrogen bonds defined for protein.
    2412 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.67

  Time building geometry restraints manager: 4.07 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2032
        1.31 -     1.43: 3909
        1.43 -     1.56: 7289
        1.56 -     1.68: 6
        1.68 -     1.81: 112
  Bond restraints: 13348
  Sorted by residual:
  bond pdb=" C7  NAG D   1 "
       pdb=" N2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.451 -0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C7  NAG C   1 "
       pdb=" N2  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.451 -0.105 2.00e-02 2.50e+03 2.74e+01
  bond pdb=" C7  NAG C   3 "
       pdb=" N2  NAG C   3 "
    ideal  model  delta    sigma   weight residual
    1.346  1.451 -0.105 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" C7  NAG D   3 "
       pdb=" N2  NAG D   3 "
    ideal  model  delta    sigma   weight residual
    1.346  1.450 -0.104 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" C7  NAG D   2 "
       pdb=" N2  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.449 -0.103 2.00e-02 2.50e+03 2.66e+01
  ... (remaining 13343 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 17899
        1.84 -     3.67: 167
        3.67 -     5.51: 58
        5.51 -     7.34: 4
        7.34 -     9.18: 4
  Bond angle restraints: 18132
  Sorted by residual:
  angle pdb=" O1B UDP A1001 "
        pdb=" PB  UDP A1001 "
        pdb=" O3A UDP A1001 "
      ideal   model   delta    sigma   weight residual
     102.95  112.13   -9.18 1.00e+00 1.00e+00 8.42e+01
  angle pdb=" O1B UDP B1001 "
        pdb=" PB  UDP B1001 "
        pdb=" O3A UDP B1001 "
      ideal   model   delta    sigma   weight residual
     102.95  112.12   -9.17 1.00e+00 1.00e+00 8.41e+01
  angle pdb=" O3A UDP A1001 "
        pdb=" PB  UDP A1001 "
        pdb=" O3B UDP A1001 "
      ideal   model   delta    sigma   weight residual
     112.01  103.03    8.98 1.00e+00 1.00e+00 8.07e+01
  angle pdb=" O3A UDP B1001 "
        pdb=" PB  UDP B1001 "
        pdb=" O3B UDP B1001 "
      ideal   model   delta    sigma   weight residual
     112.01  103.08    8.93 1.00e+00 1.00e+00 7.97e+01
  angle pdb=" O5' UDP A1001 "
        pdb=" PA  UDP A1001 "
        pdb=" O1A UDP A1001 "
      ideal   model   delta    sigma   weight residual
     106.70  111.06   -4.36 1.00e+00 1.00e+00 1.90e+01
  ... (remaining 18127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 7485
       16.84 -    33.69: 325
       33.69 -    50.53: 88
       50.53 -    67.38: 14
       67.38 -    84.22: 6
  Dihedral angle restraints: 7918
    sinusoidal: 3226
      harmonic: 4692
  Sorted by residual:
  dihedral pdb=" CA  GLN B 602 "
           pdb=" C   GLN B 602 "
           pdb=" N   GLY B 603 "
           pdb=" CA  GLY B 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.45   21.55     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  GLN A 602 "
           pdb=" C   GLN A 602 "
           pdb=" N   GLY A 603 "
           pdb=" CA  GLY A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.48   21.52     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" N   ARG B 780 "
           pdb=" CA  ARG B 780 "
           pdb=" CB  ARG B 780 "
           pdb=" CG  ARG B 780 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.30  -55.70     3      1.50e+01 4.44e-03 9.36e+00
  ... (remaining 7915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1175
       0.026 -    0.051: 525
       0.051 -    0.077: 187
       0.077 -    0.103: 73
       0.103 -    0.129: 46
  Chirality restraints: 2006
  Sorted by residual:
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.62    0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" C2  NAG C   1 "
            pdb=" C1  NAG C   1 "
            pdb=" C3  NAG C   1 "
            pdb=" N2  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.62    0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" C5  NAG D   3 "
            pdb=" C4  NAG D   3 "
            pdb=" C6  NAG D   3 "
            pdb=" O5  NAG D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.54    0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 2003 not shown)

  Planarity restraints: 2278
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 598 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   PHE B 598 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   PHE B 598 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ILE B 599 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 598 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.69e+00
        pdb=" C   PHE A 598 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PHE A 598 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 599 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 599 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" C   ILE B 599 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 599 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL B 600 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2275 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1212
        2.74 -     3.28: 12473
        3.28 -     3.82: 20996
        3.82 -     4.36: 22205
        4.36 -     4.90: 41749
  Nonbonded interactions: 98635
  Sorted by model distance:
  nonbonded pdb=" PB  UDP B1001 "
            pdb="MN    MN B1002 "
     model   vdw
     2.204 2.680
  nonbonded pdb=" PB  UDP A1001 "
            pdb="MN    MN A1002 "
     model   vdw
     2.204 2.680
  nonbonded pdb=" OH  TYR B 593 "
            pdb=" OD1 ASN B 630 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A 593 "
            pdb=" OD1 ASN A 630 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   SER A 390 "
            pdb=" ND1 HIS A 394 "
     model   vdw
     2.291 3.120
  ... (remaining 98630 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.910
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.004   0.105  13352  Z= 0.193
  Angle     :  0.524   9.177  18144  Z= 0.298
  Chirality :  0.038   0.129   2006
  Planarity :  0.003   0.026   2278
  Dihedral  : 10.756  84.223   4906
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.05 (0.22), residues: 1594
  helix:  2.87 (0.17), residues: 958
  sheet:  0.08 (0.43), residues: 156
  loop : -1.51 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 804 
 HIS   0.002   0.001   HIS A 403 
 PHE   0.012   0.001   PHE B 601 
 TYR   0.009   0.001   TYR B 365 
 ARG   0.003   0.000   ARG A 103 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00607 (    4)
  link_BETA1-4         : angle       1.68412 (   12)
  hydrogen bonds       : bond        0.12442 (  816)
  hydrogen bonds       : angle       5.13974 ( 2412)
  covalent geometry    : bond        0.00371 (13348)
  covalent geometry    : angle       0.52259 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 1.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 HIS cc_start: 0.7671 (m90) cc_final: 0.7035 (m90)
REVERT: A  179 ILE cc_start: 0.8950 (pt) cc_final: 0.8718 (mp)
REVERT: A  201 MET cc_start: 0.7951 (ptm) cc_final: 0.7652 (ppp)
REVERT: A  207 TYR cc_start: 0.8082 (t80) cc_final: 0.7578 (t80)
REVERT: A  233 MET cc_start: 0.8580 (mtp) cc_final: 0.8264 (mtp)
REVERT: A  523 THR cc_start: 0.9554 (p) cc_final: 0.9229 (t)
REVERT: A  607 ASN cc_start: 0.7617 (t0) cc_final: 0.7397 (p0)
REVERT: B   95 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: B  152 ASN cc_start: 0.8165 (m-40) cc_final: 0.7960 (m110)
REVERT: B  336 SER cc_start: 0.8419 (t) cc_final: 0.8201 (p)
REVERT: B  390 SER cc_start: 0.7996 (m) cc_final: 0.7346 (p)
REVERT: B  457 PHE cc_start: 0.7602 (t80) cc_final: 0.7253 (t80)
REVERT: B  492 TYR cc_start: 0.8499 (t80) cc_final: 0.7709 (t80)
REVERT: B  493 LEU cc_start: 0.8923 (mt) cc_final: 0.8643 (mt)
REVERT: B  607 ASN cc_start: 0.7430 (t0) cc_final: 0.7142 (t0)
REVERT: B  850 ILE cc_start: 0.8639 (tt) cc_final: 0.8437 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.2435
  time to fit residues: 105.4791
Evaluate side-chains
  181 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 145 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 605 GLN
B 141 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 605 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.112578 restraints weight = 17448.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.114949 restraints weight = 14728.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115924 restraints weight = 11983.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13352  Z= 0.231
  Angle     :  0.635   7.629  18144  Z= 0.332
  Chirality :  0.043   0.141   2006
  Planarity :  0.004   0.052   2278
  Dihedral  :  6.555  58.949   1954
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 11.97 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.22), residues: 1594
  helix:  2.33 (0.17), residues: 978
  sheet: -0.13 (0.44), residues: 150
  loop : -1.49 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 511 
 HIS   0.005   0.001   HIS A 327 
 PHE   0.017   0.002   PHE A 597 
 TYR   0.022   0.002   TYR B 575 
 ARG   0.004   0.001   ARG A 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00280 (    4)
  link_BETA1-4         : angle       2.32779 (   12)
  hydrogen bonds       : bond        0.06269 (  816)
  hydrogen bonds       : angle       4.67216 ( 2412)
  covalent geometry    : bond        0.00533 (13348)
  covalent geometry    : angle       0.63270 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 177
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.8588 (tp40) cc_final: 0.8328 (mm110)
REVERT: A  175 HIS cc_start: 0.8064 (t70) cc_final: 0.7802 (t70)
REVERT: A  201 MET cc_start: 0.7999 (ptm) cc_final: 0.7672 (ppp)
REVERT: A  207 TYR cc_start: 0.8227 (t80) cc_final: 0.7790 (t80)
REVERT: A  233 MET cc_start: 0.8836 (mtp) cc_final: 0.8420 (mtp)
REVERT: A  397 PHE cc_start: 0.8471 (t80) cc_final: 0.7794 (t80)
REVERT: A  492 TYR cc_start: 0.8656 (t80) cc_final: 0.8335 (t80)
REVERT: A  607 ASN cc_start: 0.7525 (t0) cc_final: 0.7065 (t0)
REVERT: A  694 THR cc_start: 0.8570 (t) cc_final: 0.8222 (p)
REVERT: B   95 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: B  152 ASN cc_start: 0.8282 (m-40) cc_final: 0.7949 (m110)
REVERT: B  318 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8334 (t0)
REVERT: B  390 SER cc_start: 0.8214 (m) cc_final: 0.7513 (p)
REVERT: B  492 TYR cc_start: 0.8579 (t80) cc_final: 0.7854 (t80)
REVERT: B  493 LEU cc_start: 0.9099 (mt) cc_final: 0.8618 (mt)
REVERT: B  607 ASN cc_start: 0.7797 (t0) cc_final: 0.7453 (t0)
REVERT: B  850 ILE cc_start: 0.8682 (tt) cc_final: 0.8428 (tt)
  outliers start: 48
  outliers final: 30
  residues processed: 213
  average time/residue: 0.2457
  time to fit residues: 80.0125
Evaluate side-chains
  189 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  781 GLU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  815 VAL
Chi-restraints excluded: chain B residue  844 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 117 optimal weight:    0.2980
   chunk 138 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9990
   chunk 146 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0050
   overall best weight:    0.7998

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 851 HIS
B 256 ASN
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.139360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.114691 restraints weight = 17411.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.116809 restraints weight = 14775.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.118364 restraints weight = 11525.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13352  Z= 0.135
  Angle     :  0.534  10.691  18144  Z= 0.275
  Chirality :  0.039   0.133   2006
  Planarity :  0.004   0.042   2278
  Dihedral  :  6.108  56.005   1954
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.01 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.22), residues: 1594
  helix:  2.51 (0.17), residues: 972
  sheet: -0.38 (0.42), residues: 158
  loop : -1.36 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.003   0.001   HIS B 403 
 PHE   0.015   0.001   PHE B 601 
 TYR   0.024   0.001   TYR B  88 
 ARG   0.007   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00439 (    4)
  link_BETA1-4         : angle       2.14298 (   12)
  hydrogen bonds       : bond        0.05512 (  816)
  hydrogen bonds       : angle       4.50416 ( 2412)
  covalent geometry    : bond        0.00287 (13348)
  covalent geometry    : angle       0.53151 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 167
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8507 (tp40) cc_final: 0.8281 (mm110)
REVERT: A  201 MET cc_start: 0.7977 (ptm) cc_final: 0.7716 (ppp)
REVERT: A  233 MET cc_start: 0.8726 (mtp) cc_final: 0.8326 (mtp)
REVERT: A  607 ASN cc_start: 0.7435 (t0) cc_final: 0.6985 (t0)
REVERT: A  694 THR cc_start: 0.8584 (t) cc_final: 0.8198 (p)
REVERT: B   95 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7497 (tm-30)
REVERT: B  152 ASN cc_start: 0.8232 (m-40) cc_final: 0.7964 (m110)
REVERT: B  607 ASN cc_start: 0.7780 (t0) cc_final: 0.7464 (t0)
REVERT: B  850 ILE cc_start: 0.8617 (tt) cc_final: 0.8401 (tt)
  outliers start: 42
  outliers final: 28
  residues processed: 192
  average time/residue: 0.2028
  time to fit residues: 62.5086
Evaluate side-chains
  178 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  800 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 122 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
A 647 ASN
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.140895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115397 restraints weight = 17972.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116363 restraints weight = 14957.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117499 restraints weight = 14950.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13352  Z= 0.213
  Angle     :  0.609  15.014  18144  Z= 0.313
  Chirality :  0.042   0.139   2006
  Planarity :  0.004   0.040   2278
  Dihedral  :  6.193  58.091   1954
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.53 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.22), residues: 1594
  helix:  2.27 (0.17), residues: 986
  sheet: -0.56 (0.42), residues: 158
  loop : -1.45 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 804 
 HIS   0.005   0.001   HIS B 327 
 PHE   0.019   0.001   PHE A 597 
 TYR   0.030   0.002   TYR B  88 
 ARG   0.008   0.001   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00299 (    4)
  link_BETA1-4         : angle       2.20199 (   12)
  hydrogen bonds       : bond        0.06221 (  816)
  hydrogen bonds       : angle       4.61860 ( 2412)
  covalent geometry    : bond        0.00493 (13348)
  covalent geometry    : angle       0.60660 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 159
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8598 (tp40) cc_final: 0.8358 (mm110)
REVERT: A  174 VAL cc_start: 0.9145 (t) cc_final: 0.8912 (p)
REVERT: A  201 MET cc_start: 0.8104 (ptm) cc_final: 0.7815 (ppp)
REVERT: A  233 MET cc_start: 0.8696 (mtp) cc_final: 0.8312 (mtp)
REVERT: A  492 TYR cc_start: 0.8641 (t80) cc_final: 0.8364 (t80)
REVERT: A  607 ASN cc_start: 0.7479 (t0) cc_final: 0.7043 (t0)
REVERT: B   95 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: B  102 ASP cc_start: 0.8841 (t70) cc_final: 0.8626 (t0)
REVERT: B  260 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8963 (tt)
REVERT: B  390 SER cc_start: 0.8033 (m) cc_final: 0.7381 (p)
REVERT: B  492 TYR cc_start: 0.8614 (t80) cc_final: 0.8086 (t80)
REVERT: B  607 ASN cc_start: 0.7829 (t0) cc_final: 0.7597 (t0)
  outliers start: 54
  outliers final: 43
  residues processed: 199
  average time/residue: 0.2349
  time to fit residues: 75.1395
Evaluate side-chains
  191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  781 GLU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 129 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0040
   chunk 123 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9990
   chunk 156 optimal weight:    0.4980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.145111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117052 restraints weight = 17955.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119850 restraints weight = 14824.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.121489 restraints weight = 10494.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13352  Z= 0.122
  Angle     :  0.526  13.632  18144  Z= 0.268
  Chirality :  0.039   0.148   2006
  Planarity :  0.004   0.040   2278
  Dihedral  :  5.873  54.587   1954
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.27 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.22), residues: 1594
  helix:  2.50 (0.17), residues: 972
  sheet: -0.48 (0.42), residues: 158
  loop : -1.35 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.011   0.001   HIS B 851 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.040   0.001   TYR B  88 
 ARG   0.006   0.000   ARG A 522 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00534 (    4)
  link_BETA1-4         : angle       2.17464 (   12)
  hydrogen bonds       : bond        0.05372 (  816)
  hydrogen bonds       : angle       4.46579 ( 2412)
  covalent geometry    : bond        0.00248 (13348)
  covalent geometry    : angle       0.52320 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 158
  time to evaluate  : 1.576 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8517 (tp40) cc_final: 0.8309 (mm110)
REVERT: A  201 MET cc_start: 0.7979 (ptm) cc_final: 0.7747 (ppp)
REVERT: A  443 LEU cc_start: 0.9401 (tp) cc_final: 0.9101 (tp)
REVERT: A  607 ASN cc_start: 0.7380 (t0) cc_final: 0.6906 (t0)
REVERT: A  694 THR cc_start: 0.8455 (t) cc_final: 0.8225 (p)
REVERT: B   95 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: B  492 TYR cc_start: 0.8514 (t80) cc_final: 0.8061 (t80)
REVERT: B  607 ASN cc_start: 0.7825 (t0) cc_final: 0.7538 (t0)
REVERT: B  856 ARG cc_start: 0.6028 (ttp80) cc_final: 0.5520 (tpt90)
  outliers start: 44
  outliers final: 30
  residues processed: 185
  average time/residue: 0.2447
  time to fit residues: 72.7119
Evaluate side-chains
  180 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
A 372 GLN
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.130867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.105369 restraints weight = 18723.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.106245 restraints weight = 15711.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.107742 restraints weight = 12674.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13352  Z= 0.174
  Angle     :  0.566  13.213  18144  Z= 0.289
  Chirality :  0.040   0.130   2006
  Planarity :  0.004   0.037   2278
  Dihedral  :  5.895  51.801   1954
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.78 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.22), residues: 1594
  helix:  2.38 (0.17), residues: 984
  sheet: -0.47 (0.40), residues: 168
  loop : -1.50 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.011   0.001   HIS B 851 
 PHE   0.013   0.001   PHE A 597 
 TYR   0.030   0.001   TYR B  88 
 ARG   0.007   0.000   ARG A 522 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00286 (    4)
  link_BETA1-4         : angle       2.21115 (   12)
  hydrogen bonds       : bond        0.05667 (  816)
  hydrogen bonds       : angle       4.50293 ( 2412)
  covalent geometry    : bond        0.00398 (13348)
  covalent geometry    : angle       0.56337 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 153
  time to evaluate  : 2.597 
Fit side-chains
REVERT: A   71 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.3966 (mmm)
REVERT: A  233 MET cc_start: 0.8809 (mtp) cc_final: 0.8595 (mtp)
REVERT: A  443 LEU cc_start: 0.9412 (tp) cc_final: 0.9108 (tp)
REVERT: A  607 ASN cc_start: 0.7414 (t0) cc_final: 0.6984 (t0)
REVERT: B   95 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: B  151 LEU cc_start: 0.8942 (mm) cc_final: 0.8558 (mt)
REVERT: B  492 TYR cc_start: 0.8584 (t80) cc_final: 0.8139 (t80)
REVERT: B  607 ASN cc_start: 0.7842 (t0) cc_final: 0.7637 (t0)
  outliers start: 53
  outliers final: 42
  residues processed: 189
  average time/residue: 0.2776
  time to fit residues: 84.8483
Evaluate side-chains
  192 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 2.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  781 GLU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 143 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.131525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.106027 restraints weight = 18416.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107679 restraints weight = 16259.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.108951 restraints weight = 11766.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13352  Z= 0.150
  Angle     :  0.559  14.251  18144  Z= 0.282
  Chirality :  0.039   0.128   2006
  Planarity :  0.004   0.043   2278
  Dihedral  :  5.842  50.598   1954
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.65 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.22), residues: 1594
  helix:  2.33 (0.17), residues: 998
  sheet: -0.59 (0.42), residues: 158
  loop : -1.39 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.006   0.001   HIS B 851 
 PHE   0.013   0.001   PHE B 601 
 TYR   0.025   0.001   TYR B  88 
 ARG   0.008   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00380 (    4)
  link_BETA1-4         : angle       2.18849 (   12)
  hydrogen bonds       : bond        0.05515 (  816)
  hydrogen bonds       : angle       4.47731 ( 2412)
  covalent geometry    : bond        0.00332 (13348)
  covalent geometry    : angle       0.55631 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 155
  time to evaluate  : 2.284 
Fit side-chains
REVERT: A   71 MET cc_start: 0.3937 (OUTLIER) cc_final: 0.3589 (mmm)
REVERT: A  233 MET cc_start: 0.8759 (mtp) cc_final: 0.8546 (mtp)
REVERT: A  397 PHE cc_start: 0.8525 (t80) cc_final: 0.8163 (t80)
REVERT: A  443 LEU cc_start: 0.9419 (tp) cc_final: 0.9126 (tp)
REVERT: A  607 ASN cc_start: 0.7357 (t0) cc_final: 0.6918 (t0)
REVERT: A  694 THR cc_start: 0.8476 (t) cc_final: 0.8220 (p)
REVERT: B   95 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: B  253 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8807 (tt)
REVERT: B  443 LEU cc_start: 0.9411 (tp) cc_final: 0.9165 (tp)
REVERT: B  492 TYR cc_start: 0.8527 (t80) cc_final: 0.8137 (t80)
REVERT: B  607 ASN cc_start: 0.7804 (t0) cc_final: 0.7572 (t0)
  outliers start: 54
  outliers final: 47
  residues processed: 192
  average time/residue: 0.2683
  time to fit residues: 84.2144
Evaluate side-chains
  197 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 148
  time to evaluate  : 2.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  781 GLU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  803 THR
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 146 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 134 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   chunk 121 optimal weight:    0.4980
   chunk 125 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.131273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.105560 restraints weight = 18479.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.107553 restraints weight = 17113.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.108599 restraints weight = 12162.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13352  Z= 0.161
  Angle     :  0.566  12.168  18144  Z= 0.287
  Chirality :  0.040   0.128   2006
  Planarity :  0.004   0.039   2278
  Dihedral  :  5.843  50.898   1954
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.94 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.22), residues: 1594
  helix:  2.33 (0.17), residues: 998
  sheet: -0.52 (0.40), residues: 168
  loop : -1.46 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.007   0.001   HIS B 851 
 PHE   0.012   0.001   PHE B 601 
 TYR   0.036   0.001   TYR A 207 
 ARG   0.010   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00397 (    4)
  link_BETA1-4         : angle       2.17003 (   12)
  hydrogen bonds       : bond        0.05568 (  816)
  hydrogen bonds       : angle       4.48556 ( 2412)
  covalent geometry    : bond        0.00365 (13348)
  covalent geometry    : angle       0.56317 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 153
  time to evaluate  : 4.170 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.4135 (OUTLIER) cc_final: 0.3712 (mmm)
REVERT: A  443 LEU cc_start: 0.9417 (tp) cc_final: 0.9146 (tp)
REVERT: A  607 ASN cc_start: 0.7377 (t0) cc_final: 0.6938 (t0)
REVERT: A  694 THR cc_start: 0.8431 (t) cc_final: 0.8181 (p)
REVERT: B   95 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7499 (tm-30)
REVERT: B  253 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8817 (tt)
REVERT: B  443 LEU cc_start: 0.9405 (tp) cc_final: 0.9143 (tp)
REVERT: B  492 TYR cc_start: 0.8551 (t80) cc_final: 0.8160 (t80)
REVERT: B  607 ASN cc_start: 0.7830 (t0) cc_final: 0.7612 (t0)
REVERT: B  856 ARG cc_start: 0.6018 (ttp80) cc_final: 0.5235 (tpt90)
  outliers start: 54
  outliers final: 48
  residues processed: 193
  average time/residue: 0.4578
  time to fit residues: 137.3667
Evaluate side-chains
  201 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 151
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  781 GLU
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  803 THR
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 99 optimal weight:    0.0570
   chunk 36 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 151 optimal weight:    1.9990
   chunk 104 optimal weight:    0.5980
   chunk 159 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 143 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
B 318 ASN
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.133502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.107733 restraints weight = 18350.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.109491 restraints weight = 17272.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.111211 restraints weight = 11815.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13352  Z= 0.122
  Angle     :  0.546  13.047  18144  Z= 0.273
  Chirality :  0.039   0.324   2006
  Planarity :  0.004   0.033   2278
  Dihedral  :  5.705  51.883   1954
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 19.09 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.22), residues: 1594
  helix:  2.43 (0.17), residues: 992
  sheet: -0.51 (0.41), residues: 164
  loop : -1.52 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.003   0.001   HIS B 403 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.026   0.001   TYR A 207 
 ARG   0.010   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00480 (    4)
  link_BETA1-4         : angle       2.14219 (   12)
  hydrogen bonds       : bond        0.05193 (  816)
  hydrogen bonds       : angle       4.43502 ( 2412)
  covalent geometry    : bond        0.00252 (13348)
  covalent geometry    : angle       0.54330 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 156
  time to evaluate  : 1.415 
Fit side-chains
REVERT: A   71 MET cc_start: 0.3828 (OUTLIER) cc_final: 0.3370 (mmm)
REVERT: A  397 PHE cc_start: 0.8558 (t80) cc_final: 0.8219 (t80)
REVERT: A  443 LEU cc_start: 0.9396 (tp) cc_final: 0.9130 (tp)
REVERT: A  607 ASN cc_start: 0.7322 (t0) cc_final: 0.6855 (t0)
REVERT: A  694 THR cc_start: 0.8400 (t) cc_final: 0.8195 (p)
REVERT: B   95 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7470 (tm-30)
REVERT: B  443 LEU cc_start: 0.9344 (tp) cc_final: 0.9087 (tp)
REVERT: B  492 TYR cc_start: 0.8517 (t80) cc_final: 0.8132 (t80)
REVERT: B  607 ASN cc_start: 0.7801 (t0) cc_final: 0.7551 (t0)
  outliers start: 50
  outliers final: 40
  residues processed: 192
  average time/residue: 0.2078
  time to fit residues: 63.4083
Evaluate side-chains
  192 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  800 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 129 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 145 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
B 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.126206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.102173 restraints weight = 18782.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.102932 restraints weight = 15263.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.103492 restraints weight = 12104.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13352  Z= 0.139
  Angle     :  0.562  13.660  18144  Z= 0.280
  Chirality :  0.039   0.306   2006
  Planarity :  0.004   0.047   2278
  Dihedral  :  5.687  52.225   1954
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.45 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1594
  helix:  2.42 (0.17), residues: 994
  sheet: -0.50 (0.41), residues: 164
  loop : -1.50 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 804 
 HIS   0.003   0.001   HIS B 403 
 PHE   0.014   0.001   PHE B 601 
 TYR   0.025   0.001   TYR A 207 
 ARG   0.013   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00430 (    4)
  link_BETA1-4         : angle       2.12648 (   12)
  hydrogen bonds       : bond        0.05248 (  816)
  hydrogen bonds       : angle       4.44051 ( 2412)
  covalent geometry    : bond        0.00308 (13348)
  covalent geometry    : angle       0.55966 (18132)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 155
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  443 LEU cc_start: 0.9363 (tp) cc_final: 0.9103 (tp)
REVERT: A  607 ASN cc_start: 0.7295 (t0) cc_final: 0.6840 (t0)
REVERT: A  694 THR cc_start: 0.8414 (t) cc_final: 0.8205 (p)
REVERT: B   95 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7479 (tm-30)
REVERT: B  443 LEU cc_start: 0.9359 (tp) cc_final: 0.9089 (tp)
REVERT: B  492 TYR cc_start: 0.8577 (t80) cc_final: 0.8198 (t80)
REVERT: B  607 ASN cc_start: 0.7802 (t0) cc_final: 0.7573 (t0)
  outliers start: 44
  outliers final: 41
  residues processed: 186
  average time/residue: 0.1878
  time to fit residues: 56.6849
Evaluate side-chains
  191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 150
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  800 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 159 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 127 optimal weight:    0.8980
   chunk 137 optimal weight:    4.9990
   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 175 HIS
B 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.100666 restraints weight = 18956.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.101825 restraints weight = 15281.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.103129 restraints weight = 12042.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13352  Z= 0.170
  Angle     :  0.587  13.794  18144  Z= 0.295
  Chirality :  0.041   0.306   2006
  Planarity :  0.004   0.043   2278
  Dihedral  :  5.770  52.181   1954
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 19.30 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.22), residues: 1594
  helix:  2.34 (0.17), residues: 998
  sheet: -0.55 (0.41), residues: 164
  loop : -1.49 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.004   0.001   HIS B 403 
 PHE   0.013   0.001   PHE A 597 
 TYR   0.045   0.001   TYR A 365 
 ARG   0.011   0.000   ARG B 856 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00375 (    4)
  link_BETA1-4         : angle       2.13598 (   12)
  hydrogen bonds       : bond        0.05519 (  816)
  hydrogen bonds       : angle       4.48128 ( 2412)
  covalent geometry    : bond        0.00387 (13348)
  covalent geometry    : angle       0.58490 (18132)

===============================================================================
Job complete
usr+sys time: 4070.82 seconds
wall clock time: 77 minutes 38.88 seconds (4658.88 seconds total)