Starting phenix.real_space_refine
on Thu Sep 18 01:00:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x05_32917/09_2025/7x05_32917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x05_32917/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x05_32917/09_2025/7x05_32917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x05_32917/09_2025/7x05_32917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x05_32917/09_2025/7x05_32917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x05_32917/09_2025/7x05_32917.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.70, per 1000 atoms: 0.52
  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: 1.58
  Conformation dependent library (CDL) restraints added in 627.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.48
  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: 2.55

  Time building geometry restraints manager: 1.97 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: 0.03
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:             2.470
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     17.660
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.670
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 103 
 TYR   0.009   0.001   TYR B 365 
 PHE   0.012   0.001   PHE B 601 
 TRP   0.009   0.001   TRP A 804 
 HIS   0.002   0.001   HIS A 403 

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

*********************** 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  : 0.488 
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: 0.1152
  time to fit residues: 49.8938
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  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
A 605 GLN
B 141 ASN
B 256 ASN
B 605 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.137667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.112398 restraints weight = 17500.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113804 restraints weight = 15413.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.114911 restraints weight = 13012.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115914 restraints weight = 10078.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.116035 restraints weight = 9161.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13352  Z= 0.199
  Angle     :  0.596   7.344  18144  Z= 0.311
  Chirality :  0.042   0.134   2006
  Planarity :  0.004   0.051   2278
  Dihedral  :  6.560  59.823   1954
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 11.39 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.22), residues: 1594
  helix:  2.47 (0.17), residues: 974
  sheet: -0.03 (0.44), residues: 150
  loop : -1.49 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 856 
 TYR   0.022   0.002   TYR B 575 
 PHE   0.015   0.001   PHE A 597 
 TRP   0.008   0.001   TRP B 424 
 HIS   0.004   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (13348)
  covalent geometry    : angle       0.59337 (18132)
  hydrogen bonds       : bond        0.05956 (  816)
  hydrogen bonds       : angle       4.60552 ( 2412)
  link_BETA1-4         : bond        0.00302 (    4)
  link_BETA1-4         : angle       2.21027 (   12)

*********************** 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
  227 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 178
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8514 (tp40) cc_final: 0.8257 (mm110)
REVERT: A  179 ILE cc_start: 0.8970 (pt) cc_final: 0.8695 (mp)
REVERT: A  201 MET cc_start: 0.8010 (ptm) cc_final: 0.7625 (ppp)
REVERT: A  207 TYR cc_start: 0.8181 (t80) cc_final: 0.7783 (t80)
REVERT: A  233 MET cc_start: 0.8766 (mtp) cc_final: 0.8367 (mtp)
REVERT: A  397 PHE cc_start: 0.8467 (t80) cc_final: 0.7699 (t80)
REVERT: A  492 TYR cc_start: 0.8656 (t80) cc_final: 0.8317 (t80)
REVERT: A  607 ASN cc_start: 0.7541 (t0) cc_final: 0.7072 (t0)
REVERT: A  665 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7641 (tp)
REVERT: A  694 THR cc_start: 0.8636 (t) cc_final: 0.8216 (p)
REVERT: B   95 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7457 (tm-30)
REVERT: B  152 ASN cc_start: 0.8277 (m-40) cc_final: 0.8018 (m110)
REVERT: B  318 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8340 (t0)
REVERT: B  390 SER cc_start: 0.8186 (m) cc_final: 0.7465 (p)
REVERT: B  492 TYR cc_start: 0.8553 (t80) cc_final: 0.7779 (t80)
REVERT: B  493 LEU cc_start: 0.9066 (mt) cc_final: 0.8605 (mt)
REVERT: B  607 ASN cc_start: 0.7778 (t0) cc_final: 0.7433 (t0)
REVERT: B  850 ILE cc_start: 0.8674 (tt) cc_final: 0.8408 (tt)
  outliers start: 49
  outliers final: 28
  residues processed: 213
  average time/residue: 0.0998
  time to fit residues: 32.8142
Evaluate side-chains
  185 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
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  552 TRP
Chi-restraints excluded: chain A residue  634 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 ILE
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  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 21 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 141 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
A 851 HIS
B 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115612 restraints weight = 17481.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.117030 restraints weight = 15067.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.117853 restraints weight = 12894.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.118237 restraints weight = 10520.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120097 restraints weight = 9559.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13352  Z= 0.129
  Angle     :  0.529  10.663  18144  Z= 0.272
  Chirality :  0.039   0.133   2006
  Planarity :  0.004   0.043   2278
  Dihedral  :  6.130  57.345   1954
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.72 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.22), residues: 1594
  helix:  2.56 (0.17), residues: 974
  sheet: -0.32 (0.44), residues: 152
  loop : -1.37 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 522 
 TYR   0.025   0.001   TYR B  88 
 PHE   0.014   0.001   PHE B 601 
 TRP   0.006   0.001   TRP B 804 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13348)
  covalent geometry    : angle       0.52680 (18132)
  hydrogen bonds       : bond        0.05363 (  816)
  hydrogen bonds       : angle       4.47953 ( 2412)
  link_BETA1-4         : bond        0.00471 (    4)
  link_BETA1-4         : angle       2.10424 (   12)

*********************** 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
  204 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 165
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  179 ILE cc_start: 0.8907 (pt) cc_final: 0.8670 (mp)
REVERT: A  201 MET cc_start: 0.7967 (ptm) cc_final: 0.7631 (ppp)
REVERT: A  207 TYR cc_start: 0.8208 (t80) cc_final: 0.7811 (t80)
REVERT: A  233 MET cc_start: 0.8686 (mtp) cc_final: 0.8295 (mtp)
REVERT: A  397 PHE cc_start: 0.8430 (t80) cc_final: 0.7760 (t80)
REVERT: A  607 ASN cc_start: 0.7409 (t0) cc_final: 0.6945 (t0)
REVERT: A  694 THR cc_start: 0.8562 (t) cc_final: 0.8136 (p)
REVERT: B   95 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7448 (tm-30)
REVERT: B  152 ASN cc_start: 0.8189 (m-40) cc_final: 0.7971 (m110)
REVERT: B  291 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7157 (t0)
REVERT: B  390 SER cc_start: 0.7983 (m) cc_final: 0.7294 (p)
REVERT: B  607 ASN cc_start: 0.7735 (t0) cc_final: 0.7399 (t0)
REVERT: B  850 ILE cc_start: 0.8573 (tt) cc_final: 0.8368 (tt)
  outliers start: 39
  outliers final: 23
  residues processed: 189
  average time/residue: 0.0876
  time to fit residues: 26.4442
Evaluate side-chains
  176 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
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  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  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  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 156 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 138 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 150 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 159 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 851 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.143732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116539 restraints weight = 18085.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118979 restraints weight = 12901.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120170 restraints weight = 10860.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.120870 restraints weight = 8236.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121147 restraints weight = 7958.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13352  Z= 0.146
  Angle     :  0.534  13.879  18144  Z= 0.273
  Chirality :  0.039   0.131   2006
  Planarity :  0.004   0.039   2278
  Dihedral  :  5.962  55.882   1954
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.37 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.22), residues: 1594
  helix:  2.60 (0.17), residues: 972
  sheet: -0.30 (0.43), residues: 158
  loop : -1.30 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 856 
 TYR   0.031   0.001   TYR B  88 
 PHE   0.012   0.001   PHE B 601 
 TRP   0.006   0.001   TRP B 424 
 HIS   0.003   0.001   HIS B 514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13348)
  covalent geometry    : angle       0.53126 (18132)
  hydrogen bonds       : bond        0.05379 (  816)
  hydrogen bonds       : angle       4.45056 ( 2412)
  link_BETA1-4         : bond        0.00390 (    4)
  link_BETA1-4         : angle       2.17110 (   12)

*********************** 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
  206 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 163
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8448 (tp40) cc_final: 0.8237 (mm110)
REVERT: A  179 ILE cc_start: 0.8930 (pt) cc_final: 0.8695 (mp)
REVERT: A  201 MET cc_start: 0.7971 (ptm) cc_final: 0.7766 (ppp)
REVERT: A  233 MET cc_start: 0.8624 (mtp) cc_final: 0.8291 (mtp)
REVERT: A  607 ASN cc_start: 0.7381 (t0) cc_final: 0.6888 (t0)
REVERT: A  694 THR cc_start: 0.8433 (t) cc_final: 0.8057 (p)
REVERT: A  831 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7928 (t80)
REVERT: B   95 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7516 (tm-30)
REVERT: B  260 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8857 (tt)
REVERT: B  291 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7247 (t0)
REVERT: B  390 SER cc_start: 0.7964 (m) cc_final: 0.7329 (p)
REVERT: B  492 TYR cc_start: 0.8483 (t80) cc_final: 0.8003 (t80)
REVERT: B  607 ASN cc_start: 0.7742 (t0) cc_final: 0.7436 (t0)
  outliers start: 43
  outliers final: 30
  residues processed: 192
  average time/residue: 0.0877
  time to fit residues: 27.1902
Evaluate side-chains
  186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 153
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  253 LEU
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  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  719 THR
Chi-restraints excluded: chain A residue  797 ARG
Chi-restraints excluded: chain A residue  831 PHE
Chi-restraints excluded: chain A residue  851 HIS
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  333 LEU
Chi-restraints excluded: chain B residue  336 SER
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  639 MET
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  722 ILE
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 71 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 158 optimal weight:    4.9990
   chunk 144 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 132 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 175 HIS
B 152 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 = 0.3592 r_free = 0.3592 target = 0.139710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.113741 restraints weight = 18298.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.114581 restraints weight = 13920.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.115857 restraints weight = 13259.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116661 restraints weight = 9363.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.116994 restraints weight = 9017.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13352  Z= 0.220
  Angle     :  0.609  13.849  18144  Z= 0.314
  Chirality :  0.042   0.138   2006
  Planarity :  0.004   0.047   2278
  Dihedral  :  6.147  58.405   1954
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.04 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.22), residues: 1594
  helix:  2.33 (0.17), residues: 984
  sheet: -0.53 (0.42), residues: 158
  loop : -1.42 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 856 
 TYR   0.021   0.002   TYR B  88 
 PHE   0.019   0.001   PHE A 597 
 TRP   0.008   0.001   TRP B 804 
 HIS   0.018   0.001   HIS B 851 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (13348)
  covalent geometry    : angle       0.60644 (18132)
  hydrogen bonds       : bond        0.06100 (  816)
  hydrogen bonds       : angle       4.59485 ( 2412)
  link_BETA1-4         : bond        0.00304 (    4)
  link_BETA1-4         : angle       2.17849 (   12)

*********************** 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
  203 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 153
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A   54 THR cc_start: 0.7894 (m) cc_final: 0.7693 (p)
REVERT: A  201 MET cc_start: 0.8096 (ptm) cc_final: 0.7817 (ppp)
REVERT: A  207 TYR cc_start: 0.8515 (t80) cc_final: 0.8208 (t80)
REVERT: A  233 MET cc_start: 0.8687 (mtp) cc_final: 0.8324 (mtp)
REVERT: A  492 TYR cc_start: 0.8635 (t80) cc_final: 0.8382 (t80)
REVERT: A  607 ASN cc_start: 0.7445 (t0) cc_final: 0.7004 (t0)
REVERT: B   95 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: B  102 ASP cc_start: 0.8823 (t70) cc_final: 0.8615 (t0)
REVERT: B  260 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8930 (tt)
REVERT: B  492 TYR cc_start: 0.8571 (t80) cc_final: 0.8119 (t80)
REVERT: B  607 ASN cc_start: 0.7808 (t0) cc_final: 0.7558 (t0)
  outliers start: 50
  outliers final: 37
  residues processed: 191
  average time/residue: 0.0927
  time to fit residues: 28.2863
Evaluate side-chains
  186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
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  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  850 ILE
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  260 LEU
Chi-restraints excluded: chain B residue  291 ASP
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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 144 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 124 optimal weight:    0.0970
   chunk 87 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
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 = 0.3674 r_free = 0.3674 target = 0.146572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118501 restraints weight = 17932.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.121740 restraints weight = 13585.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.123162 restraints weight = 9576.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123638 restraints weight = 7642.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124107 restraints weight = 7261.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13352  Z= 0.118
  Angle     :  0.533  12.457  18144  Z= 0.269
  Chirality :  0.038   0.139   2006
  Planarity :  0.004   0.039   2278
  Dihedral  :  5.768  53.000   1954
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.34 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.22), residues: 1594
  helix:  2.56 (0.17), residues: 970
  sheet: -0.35 (0.43), residues: 156
  loop : -1.35 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 856 
 TYR   0.036   0.001   TYR B  88 
 PHE   0.016   0.001   PHE B 601 
 TRP   0.007   0.001   TRP B 153 
 HIS   0.004   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (13348)
  covalent geometry    : angle       0.52974 (18132)
  hydrogen bonds       : bond        0.05172 (  816)
  hydrogen bonds       : angle       4.43326 ( 2412)
  link_BETA1-4         : bond        0.00497 (    4)
  link_BETA1-4         : angle       2.19376 (   12)

*********************** 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: 44
    poor density    : 162
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8584 (tp40) cc_final: 0.8360 (mm110)
REVERT: A  207 TYR cc_start: 0.8436 (t80) cc_final: 0.8026 (t80)
REVERT: A  443 LEU cc_start: 0.9418 (tp) cc_final: 0.9147 (tp)
REVERT: A  607 ASN cc_start: 0.7254 (t0) cc_final: 0.6768 (t0)
REVERT: A  694 THR cc_start: 0.8304 (t) cc_final: 0.8101 (p)
REVERT: B   95 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: B  492 TYR cc_start: 0.8446 (t80) cc_final: 0.8058 (t80)
REVERT: B  607 ASN cc_start: 0.7741 (t0) cc_final: 0.7408 (t0)
REVERT: B  856 ARG cc_start: 0.5757 (ttp80) cc_final: 0.5236 (tpt90)
  outliers start: 44
  outliers final: 29
  residues processed: 190
  average time/residue: 0.0927
  time to fit residues: 28.1114
Evaluate side-chains
  184 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  318 ASN
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  634 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  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  665 LEU
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  722 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 103 optimal weight:    0.4980
   chunk 131 optimal weight:    0.9990
   chunk 134 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 145 optimal weight:    1.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.143403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.118498 restraints weight = 18043.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118584 restraints weight = 15605.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120553 restraints weight = 14670.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.121168 restraints weight = 9929.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.121625 restraints weight = 9431.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13352  Z= 0.169
  Angle     :  0.570  12.124  18144  Z= 0.291
  Chirality :  0.040   0.128   2006
  Planarity :  0.004   0.036   2278
  Dihedral  :  5.835  50.665   1954
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.43 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1594
  helix:  2.34 (0.17), residues: 998
  sheet: -0.43 (0.41), residues: 168
  loop : -1.40 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 522 
 TYR   0.029   0.001   TYR B  88 
 PHE   0.029   0.001   PHE A 611 
 TRP   0.011   0.001   TRP A 554 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (13348)
  covalent geometry    : angle       0.56693 (18132)
  hydrogen bonds       : bond        0.05579 (  816)
  hydrogen bonds       : angle       4.49058 ( 2412)
  link_BETA1-4         : bond        0.00362 (    4)
  link_BETA1-4         : angle       2.17880 (   12)

*********************** 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
  194 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8540 (t80) cc_final: 0.8111 (t80)
REVERT: A  233 MET cc_start: 0.8731 (mtp) cc_final: 0.8513 (mtp)
REVERT: A  607 ASN cc_start: 0.7348 (t0) cc_final: 0.6894 (t0)
REVERT: A  694 THR cc_start: 0.8430 (t) cc_final: 0.8165 (p)
REVERT: B   95 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7606 (tm-30)
REVERT: B  492 TYR cc_start: 0.8569 (t80) cc_final: 0.8182 (t80)
REVERT: B  607 ASN cc_start: 0.7825 (t0) cc_final: 0.7567 (t0)
  outliers start: 42
  outliers final: 38
  residues processed: 184
  average time/residue: 0.0935
  time to fit residues: 27.5559
Evaluate side-chains
  185 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 147
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
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  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  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  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  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  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  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  851 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 156 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 150 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.144612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.118688 restraints weight = 17823.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.119322 restraints weight = 14927.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.121125 restraints weight = 14464.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121547 restraints weight = 10110.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122000 restraints weight = 9787.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3083

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= 0.140
  Angle     :  0.551  11.333  18144  Z= 0.279
  Chirality :  0.039   0.296   2006
  Planarity :  0.004   0.042   2278
  Dihedral  :  5.767  51.255   1954
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.58 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.23), residues: 1594
  helix:  2.37 (0.17), residues: 998
  sheet: -0.44 (0.41), residues: 168
  loop : -1.40 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 856 
 TYR   0.026   0.001   TYR B  88 
 PHE   0.027   0.001   PHE A 611 
 TRP   0.008   0.001   TRP A 554 
 HIS   0.006   0.001   HIS B 851 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13348)
  covalent geometry    : angle       0.54863 (18132)
  hydrogen bonds       : bond        0.05353 (  816)
  hydrogen bonds       : angle       4.45103 ( 2412)
  link_BETA1-4         : bond        0.00488 (    4)
  link_BETA1-4         : angle       2.15710 (   12)

*********************** 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
  196 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8524 (t80) cc_final: 0.8191 (t80)
REVERT: A  233 MET cc_start: 0.8719 (mtp) cc_final: 0.8489 (mtp)
REVERT: A  443 LEU cc_start: 0.9423 (tp) cc_final: 0.9154 (tp)
REVERT: A  607 ASN cc_start: 0.7323 (t0) cc_final: 0.6849 (t0)
REVERT: B   95 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: B  492 TYR cc_start: 0.8508 (t80) cc_final: 0.8160 (t80)
REVERT: B  495 GLU cc_start: 0.8293 (mp0) cc_final: 0.8075 (mp0)
REVERT: B  607 ASN cc_start: 0.7790 (t0) cc_final: 0.7526 (t0)
REVERT: B  856 ARG cc_start: 0.6008 (ttp80) cc_final: 0.5227 (tpt90)
  outliers start: 44
  outliers final: 39
  residues processed: 186
  average time/residue: 0.0883
  time to fit residues: 26.5360
Evaluate side-chains
  191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  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  396 LEU
Chi-restraints excluded: chain A residue  435 ILE
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  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  669 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  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  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  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  719 THR
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  800 VAL
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 42 optimal weight:    2.9990
   chunk 127 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 131 optimal weight:    0.6980
   chunk 138 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   chunk 137 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.145371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.119056 restraints weight = 17985.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.121287 restraints weight = 15108.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.122826 restraints weight = 11971.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123250 restraints weight = 8951.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.123672 restraints weight = 8463.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13352  Z= 0.130
  Angle     :  0.542  10.745  18144  Z= 0.275
  Chirality :  0.039   0.296   2006
  Planarity :  0.004   0.034   2278
  Dihedral  :  5.698  51.914   1954
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.87 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.23), residues: 1594
  helix:  2.41 (0.17), residues: 998
  sheet: -0.40 (0.41), residues: 168
  loop : -1.37 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 856 
 TYR   0.025   0.001   TYR B  88 
 PHE   0.027   0.001   PHE A 611 
 TRP   0.006   0.001   TRP B 804 
 HIS   0.004   0.001   HIS B 851 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (13348)
  covalent geometry    : angle       0.53974 (18132)
  hydrogen bonds       : bond        0.05198 (  816)
  hydrogen bonds       : angle       4.43310 ( 2412)
  link_BETA1-4         : bond        0.00436 (    4)
  link_BETA1-4         : angle       2.15635 (   12)

*********************** 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: 45
    poor density    : 161
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8521 (t80) cc_final: 0.8209 (t80)
REVERT: A  233 MET cc_start: 0.8669 (mtp) cc_final: 0.8466 (mtp)
REVERT: A  443 LEU cc_start: 0.9403 (tp) cc_final: 0.9131 (tp)
REVERT: A  607 ASN cc_start: 0.7312 (t0) cc_final: 0.6815 (t0)
REVERT: A  694 THR cc_start: 0.8386 (t) cc_final: 0.8152 (p)
REVERT: B   95 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: B  313 ASP cc_start: 0.8057 (m-30) cc_final: 0.7685 (m-30)
REVERT: B  443 LEU cc_start: 0.9382 (tp) cc_final: 0.9140 (tp)
REVERT: B  492 TYR cc_start: 0.8494 (t80) cc_final: 0.8140 (t80)
REVERT: B  607 ASN cc_start: 0.7794 (t0) cc_final: 0.7495 (t0)
  outliers start: 45
  outliers final: 40
  residues processed: 197
  average time/residue: 0.0917
  time to fit residues: 29.1827
Evaluate side-chains
  191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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  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  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  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  669 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  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  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  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  719 THR
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 136 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 146 optimal weight:    3.9990
   chunk 137 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 110 optimal weight:    8.9990
   chunk 129 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.145474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.119740 restraints weight = 18080.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120181 restraints weight = 14201.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122394 restraints weight = 12961.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.122786 restraints weight = 9398.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.122975 restraints weight = 9499.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3170

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= 0.134
  Angle     :  0.550  12.408  18144  Z= 0.277
  Chirality :  0.039   0.293   2006
  Planarity :  0.004   0.045   2278
  Dihedral  :  5.667  52.294   1954
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.87 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.23), residues: 1594
  helix:  2.40 (0.17), residues: 998
  sheet: -0.53 (0.43), residues: 154
  loop : -1.33 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 856 
 TYR   0.024   0.001   TYR B  88 
 PHE   0.028   0.001   PHE A 611 
 TRP   0.006   0.001   TRP B 804 
 HIS   0.006   0.001   HIS B 851 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13348)
  covalent geometry    : angle       0.54755 (18132)
  hydrogen bonds       : bond        0.05174 (  816)
  hydrogen bonds       : angle       4.43698 ( 2412)
  link_BETA1-4         : bond        0.00402 (    4)
  link_BETA1-4         : angle       2.14297 (   12)

********************** 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
  198 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8514 (t80) cc_final: 0.8231 (t80)
REVERT: A  443 LEU cc_start: 0.9409 (tp) cc_final: 0.9143 (tp)
REVERT: A  607 ASN cc_start: 0.7306 (t0) cc_final: 0.6825 (t0)
REVERT: A  694 THR cc_start: 0.8439 (t) cc_final: 0.8225 (p)
REVERT: B   95 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: B  313 ASP cc_start: 0.8016 (m-30) cc_final: 0.7673 (m-30)
REVERT: B  443 LEU cc_start: 0.9358 (tp) cc_final: 0.9109 (tp)
REVERT: B  492 TYR cc_start: 0.8515 (t80) cc_final: 0.8167 (t80)
REVERT: B  607 ASN cc_start: 0.7788 (t0) cc_final: 0.7523 (t0)
  outliers start: 44
  outliers final: 41
  residues processed: 187
  average time/residue: 0.0887
  time to fit residues: 27.1525
Evaluate side-chains
  195 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 154
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  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  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  669 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  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  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  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  719 THR
Chi-restraints excluded: chain B residue  722 ILE
Chi-restraints excluded: chain B residue  800 VAL
Chi-restraints excluded: chain B residue  851 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 141 optimal weight:    0.0050
   chunk 20 optimal weight:    0.8980
   chunk 154 optimal weight:    1.9990
   chunk 142 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0270
   chunk 24 optimal weight:    0.1980
   overall best weight:    0.1710

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.149312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.121324 restraints weight = 17880.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.124702 restraints weight = 14116.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126114 restraints weight = 9938.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126798 restraints weight = 7630.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.127123 restraints weight = 7390.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3214

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= 0.110
  Angle     :  0.535  14.919  18144  Z= 0.267
  Chirality :  0.038   0.284   2006
  Planarity :  0.004   0.036   2278
  Dihedral  :  5.459  53.174   1954
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.17 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.23), residues: 1594
  helix:  2.53 (0.17), residues: 994
  sheet: -0.26 (0.44), residues: 150
  loop : -1.39 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 856 
 TYR   0.022   0.001   TYR B  88 
 PHE   0.026   0.001   PHE A 611 
 TRP   0.006   0.001   TRP B 804 
 HIS   0.016   0.001   HIS B 851 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (13348)
  covalent geometry    : angle       0.53276 (18132)
  hydrogen bonds       : bond        0.04612 (  816)
  hydrogen bonds       : angle       4.37501 ( 2412)
  link_BETA1-4         : bond        0.00559 (    4)
  link_BETA1-4         : angle       2.08447 (   12)

===============================================================================
Job complete
usr+sys time: 1812.69 seconds
wall clock time: 32 minutes 19.53 seconds (1939.53 seconds total)