Starting phenix.real_space_refine
on Tue Jul 29 05:35:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ou2_13073/07_2025/7ou2_13073_neut.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.022 sd=   0.074
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      54      5.16       5
     C    6781      2.51       5
     N    1916      2.21       5
     O    2043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10798
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 721, 5632
          Classifications: {'peptide': 721}
          Link IDs: {'PTRANS': 33, 'TRANS': 687}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 650, 5112
          Classifications: {'peptide': 650}
          Link IDs: {'PTRANS': 27, 'TRANS': 622}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.45, per 1000 atoms: 0.69
  Number of scatterers: 10798
  At special positions: 0
  Unit cell: (117.66, 99.64, 127.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       4     15.00
     O    2043      8.00
     N    1916      7.00
     C    6781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 10 sheets defined
      55.1% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 24
      removed outlier: 3.546A  pdb=" N   HIS A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 75 through 86
      removed outlier: 3.758A  pdb=" N   TYR A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 4.063A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 3.651A  pdb=" N   GLU A 203 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 218
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.650A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 266
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 290 through 296
    Processing helix  chain 'A' and resid 300 through 313
    Processing helix  chain 'A' and resid 317 through 332
      removed outlier: 3.687A  pdb=" N   LEU A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 344
      Proline residue:  A 340  - end of helix
      removed outlier: 3.744A  pdb=" N   GLN A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
    Processing helix  chain 'A' and resid 361 through 385
      Proline residue:  A 376  - end of helix
      removed outlier: 3.696A  pdb=" N   THR A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.987A  pdb=" N   GLY A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 430 through 444
      removed outlier: 3.815A  pdb=" N   ALA A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 536
      removed outlier: 3.618A  pdb=" N   PHE A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 565
    Processing helix  chain 'A' and resid 585 through 592
    Processing helix  chain 'A' and resid 619 through 635
      removed outlier: 3.504A  pdb=" N   TYR A 623 " --> pdb=" O   GLY A 619 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   MET A 624 " --> pdb=" O   LYS A 620 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 627 " --> pdb=" O   TYR A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 684
    Processing helix  chain 'A' and resid 700 through 718
    Processing helix  chain 'A' and resid 731 through 733
      No H-bonds generated for 'chain 'A' and resid 731 through 733'
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 770 through 778
      removed outlier: 4.326A  pdb=" N   ALA A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
    Processing helix  chain 'B' and resid 18 through 24
      removed outlier: 3.615A  pdb=" N   HIS B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 51
    Processing helix  chain 'B' and resid 72 through 74
      No H-bonds generated for 'chain 'B' and resid 72 through 74'
    Processing helix  chain 'B' and resid 75 through 86
      removed outlier: 3.685A  pdb=" N   TYR B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 4.107A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 204
      removed outlier: 3.650A  pdb=" N   GLU B 203 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.664A  pdb=" N   ALA B 236 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 266
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.521A  pdb=" N   ARG B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 300 through 313
      removed outlier: 3.511A  pdb=" N   SER B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 333
      removed outlier: 3.711A  pdb=" N   LEU B 321 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 344
      Proline residue:  B 340  - end of helix
      removed outlier: 3.716A  pdb=" N   GLN B 344 " --> pdb=" O   PRO B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 357
    Processing helix  chain 'B' and resid 361 through 385
      Proline residue:  B 376  - end of helix
      removed outlier: 3.619A  pdb=" N   THR B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 521 through 536
    Processing helix  chain 'B' and resid 538 through 565
    Processing helix  chain 'B' and resid 587 through 591
    Processing helix  chain 'B' and resid 619 through 636
      removed outlier: 4.183A  pdb=" N   MET B 624 " --> pdb=" O   LYS B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 684
    Processing helix  chain 'B' and resid 700 through 718
    Processing helix  chain 'B' and resid 731 through 733
      No H-bonds generated for 'chain 'B' and resid 731 through 733'
    Processing helix  chain 'B' and resid 734 through 739
    Processing helix  chain 'B' and resid 770 through 778
      removed outlier: 3.974A  pdb=" N   ALA B 774 " --> pdb=" O   SER B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 800
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.388A  pdb=" N   ILE A  66 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A  31 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   CYS A  93 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   PHE A  30 " --> pdb=" O   CYS A  93 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   GLN A  95 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 8.830A  pdb=" N   ARG A  32 " --> pdb=" O   GLN A  95 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   VAL A 110 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.614A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 9.171A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   ILE A 136 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269
      removed outlier: 6.926A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 8.415A  pdb=" N   THR A 655 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ARG A 652 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LEU A 691 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ASP A 693 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ARG A 656 " --> pdb=" O   ASP A 693 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 572
      removed outlier: 6.683A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A 644 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLU A 582 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   ASN A 599 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 609 through 613
      removed outlier: 6.798A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   THR A 613 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   ALA A 749 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP A 748 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER A 761 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU A 750 " --> pdb=" O   MET A 759 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   MET A 759 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   HIS A 752 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   ALA A 757 " --> pdb=" O   HIS A 752 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69
      removed outlier: 3.803A  pdb=" N   TYR B  31 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   PHE B  40 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   LEU B  29 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B  32 " --> pdb=" O   CYS B  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199
      removed outlier: 6.622A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR B 180 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 9.191A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   ILE B 136 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 269
      removed outlier: 6.791A  pdb=" N   ILE B 268 " --> pdb=" O   ILE B 653 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   THR B 655 " --> pdb=" O   ILE B 268 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ARG B 652 " --> pdb=" O   LEU B 689 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU B 691 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   MET B 692 " --> pdb=" O   LEU B 724 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 571 through 572
      removed outlier: 6.769A  pdb=" N   THR B 571 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS B 644 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 582 " --> pdb=" O   ASN B 599 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ASN B 599 " --> pdb=" O   GLU B 582 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 750 through 752

    552 hydrogen bonds defined for protein.
    1557 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: 3.71

  Time building geometry restraints manager: 3.16 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: 1839
        1.31 -     1.43: 2689
        1.43 -     1.56: 6346
        1.56 -     1.69: 6
        1.69 -     1.82: 96
  Bond restraints: 10976
  Sorted by residual:
  bond pdb=" C4  ADP A1801 "
       pdb=" C5  ADP A1801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.378  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C4  ADP B1801 "
       pdb=" C5  ADP B1801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" N   ARG A 199 "
       pdb=" CA  ARG A 199 "
    ideal  model  delta    sigma   weight residual
    1.453  1.495 -0.042 8.30e-03 1.45e+04 2.51e+01
  bond pdb=" N   ARG B 199 "
       pdb=" CA  ARG B 199 "
    ideal  model  delta    sigma   weight residual
    1.453  1.493 -0.040 8.30e-03 1.45e+04 2.30e+01
  bond pdb=" C   PRO B 615 "
       pdb=" O   PRO B 615 "
    ideal  model  delta    sigma   weight residual
    1.233  1.177  0.056 1.19e-02 7.06e+03 2.21e+01
  ... (remaining 10971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 12295
        2.51 -     5.03: 2462
        5.03 -     7.54: 88
        7.54 -    10.05: 23
       10.05 -    12.56: 1
  Bond angle restraints: 14869
  Sorted by residual:
  angle pdb=" N   CYS B 297 "
        pdb=" CA  CYS B 297 "
        pdb=" C   CYS B 297 "
      ideal   model   delta    sigma   weight residual
     111.56  101.89    9.67 1.38e+00 5.25e-01 4.91e+01
  angle pdb=" N   CYS A 297 "
        pdb=" CA  CYS A 297 "
        pdb=" C   CYS A 297 "
      ideal   model   delta    sigma   weight residual
     111.71  102.87    8.84 1.34e+00 5.57e-01 4.35e+01
  angle pdb=" C   THR B 669 "
        pdb=" CA  THR B 669 "
        pdb=" CB  THR B 669 "
      ideal   model   delta    sigma   weight residual
     110.88  101.06    9.82 1.57e+00 4.06e-01 3.91e+01
  angle pdb=" N   ARG A 697 "
        pdb=" CA  ARG A 697 "
        pdb=" C   ARG A 697 "
      ideal   model   delta    sigma   weight residual
     112.93  106.08    6.85 1.12e+00 7.97e-01 3.74e+01
  angle pdb=" N   ILE A 636 "
        pdb=" CA  ILE A 636 "
        pdb=" C   ILE A 636 "
      ideal   model   delta    sigma   weight residual
     112.80  105.92    6.88 1.15e+00 7.56e-01 3.58e+01
  ... (remaining 14864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.73: 6456
       26.73 -    53.45: 244
       53.45 -    80.18: 26
       80.18 -   106.91: 3
      106.91 -   133.63: 3
  Dihedral angle restraints: 6732
    sinusoidal: 2754
      harmonic: 3978
  Sorted by residual:
  dihedral pdb=" O2A ADP A1801 "
           pdb=" O3A ADP A1801 "
           pdb=" PA  ADP A1801 "
           pdb=" PB  ADP A1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   73.64 -133.63     1      2.00e+01 2.50e-03 4.06e+01
  dihedral pdb=" O2A ADP B1801 "
           pdb=" O3A ADP B1801 "
           pdb=" PA  ADP B1801 "
           pdb=" PB  ADP B1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   60.77 -120.77     1      2.00e+01 2.50e-03 3.63e+01
  dihedral pdb=" O1B ADP B1801 "
           pdb=" O3A ADP B1801 "
           pdb=" PB  ADP B1801 "
           pdb=" PA  ADP B1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  179.79  120.21     1      2.00e+01 2.50e-03 3.61e+01
  ... (remaining 6729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 768
       0.081 -    0.163: 641
       0.163 -    0.244: 252
       0.244 -    0.325: 42
       0.325 -    0.406: 3
  Chirality restraints: 1706
  Sorted by residual:
  chirality pdb=" CA  TYR B 528 "
            pdb=" N   TYR B 528 "
            pdb=" C   TYR B 528 "
            pdb=" CB  TYR B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CA  TYR B 635 "
            pdb=" N   TYR B 635 "
            pdb=" C   TYR B 635 "
            pdb=" CB  TYR B 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.83e+00
  chirality pdb=" CA  TYR A 635 "
            pdb=" N   TYR A 635 "
            pdb=" C   TYR A 635 "
            pdb=" CB  TYR A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  ... (remaining 1703 not shown)

  Planarity restraints: 1934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 275 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   ARG B 275 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ARG B 275 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASN B 276 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 642 "   -0.016 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   ALA B 642 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ALA B 642 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN B 643 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 378 "   -0.015 2.00e-02 2.50e+03   3.09e-02 9.53e+00
        pdb=" C   LEU A 378 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LEU A 378 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 379 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1931 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 4421
        2.95 -     3.44: 11219
        3.44 -     3.93: 18368
        3.93 -     4.41: 20845
        4.41 -     4.90: 33099
  Nonbonded interactions: 87952
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 139 "
            pdb=" O   ASP A 139 "
     model   vdw
     2.465 2.496
  nonbonded pdb=" N   VAL B 781 "
            pdb=" O   VAL B 781 "
     model   vdw
     2.473 2.496
  nonbonded pdb=" N   VAL A 781 "
            pdb=" O   VAL A 781 "
     model   vdw
     2.486 2.496
  nonbonded pdb=" N   ASP B 139 "
            pdb=" O   ASP B 139 "
     model   vdw
     2.489 2.496
  nonbonded pdb=" N   THR A  56 "
            pdb=" O   THR A  56 "
     model   vdw
     2.510 2.496
  ... (remaining 87947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 17 through 56 or resid 67 through 94 or resid 109 through  \ 
412 or resid 520 through 800 or resid 1801))
  selection = (chain 'B' and (resid 17 through 662 or resid 667 through 800 or resid 1801))
}

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:             9.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          1.330
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.000
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6411
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.112  10976  Z= 0.995
  Angle     :  1.801  12.564  14869  Z= 1.382
  Chirality :  0.120   0.406   1706
  Planarity :  0.008   0.034   1934
  Dihedral  : 14.072 133.634   4156
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.21), residues: 1355
  helix:  2.66 (0.18), residues: 649
  sheet: -0.52 (0.37), residues: 148
  loop : -0.55 (0.23), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP A 137 
 HIS   0.007   0.002   HIS B 312 
 PHE   0.021   0.004   PHE A 730 
 TYR   0.037   0.005   TYR B 528 
 ARG   0.025   0.002   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21782 (  552)
  hydrogen bonds       : angle       6.80673 ( 1557)
  covalent geometry    : bond        0.01308 (10976)
  covalent geometry    : angle       1.80104 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 365
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9234 (m) cc_final: 0.8768 (p)
REVERT: A  260 MET cc_start: 0.6887 (tpt) cc_final: 0.6471 (tpp)
REVERT: A  323 GLU cc_start: 0.8661 (tt0) cc_final: 0.8196 (tm-30)
REVERT: A  365 LEU cc_start: 0.8581 (mt) cc_final: 0.7161 (mt)
REVERT: A  441 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (p0)
REVERT: A  528 TYR cc_start: 0.6743 (t80) cc_final: 0.6098 (t80)
REVERT: A  552 LEU cc_start: 0.9147 (tp) cc_final: 0.8843 (mp)
REVERT: A  615 PRO cc_start: 0.6031 (Cg_endo) cc_final: 0.3607 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8204 (mmm) cc_final: 0.7295 (mmt)
REVERT: A  740 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8134 (pm20)
REVERT: B   73 TYR cc_start: 0.5483 (p90) cc_final: 0.5127 (p90)
REVERT: B  157 LEU cc_start: 0.7350 (tp) cc_final: 0.6803 (pp)
REVERT: B  158 SER cc_start: 0.5808 (p) cc_final: 0.5407 (t)
REVERT: B  173 THR cc_start: 0.7410 (p) cc_final: 0.6974 (t)
REVERT: B  333 ASP cc_start: 0.8353 (m-30) cc_final: 0.7833 (t0)
REVERT: B  368 MET cc_start: 0.7736 (ttm) cc_final: 0.7527 (ttm)
REVERT: B  524 GLU cc_start: 0.7075 (pt0) cc_final: 0.6849 (mm-30)
REVERT: B  602 ASN cc_start: 0.7724 (m-40) cc_final: 0.7449 (m-40)
REVERT: B  687 TYR cc_start: 0.7565 (m-80) cc_final: 0.7021 (m-80)
REVERT: B  718 LYS cc_start: 0.7581 (mttp) cc_final: 0.7194 (tmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 366
  average time/residue: 0.4482
  time to fit residues: 216.3037
Evaluate side-chains
  236 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 79 optimal weight:    0.3980
   chunk 124 optimal weight:    7.9990
   overall best weight:    5.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
A 326 GLN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 683 ASN
B 171 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 760 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.076522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.067402 restraints weight = 70213.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.068859 restraints weight = 51072.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.069964 restraints weight = 38833.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10976  Z= 0.192
  Angle     :  0.766  10.176  14869  Z= 0.394
  Chirality :  0.045   0.174   1706
  Planarity :  0.006   0.098   1934
  Dihedral  :  7.397 123.110   1532
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.43 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.21), residues: 1355
  helix:  1.52 (0.19), residues: 665
  sheet: -0.56 (0.34), residues: 178
  loop : -0.61 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 709 
 HIS   0.009   0.002   HIS B 370 
 PHE   0.029   0.002   PHE B 155 
 TYR   0.033   0.003   TYR B 528 
 ARG   0.015   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04810 (  552)
  hydrogen bonds       : angle       5.11094 ( 1557)
  covalent geometry    : bond        0.00423 (10976)
  covalent geometry    : angle       0.76643 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 268
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.7189 (mttp) cc_final: 0.6900 (mttp)
REVERT: A   83 LEU cc_start: 0.7731 (mt) cc_final: 0.7509 (mt)
REVERT: A  133 LEU cc_start: 0.7920 (tp) cc_final: 0.7402 (tp)
REVERT: A  155 PHE cc_start: 0.8238 (t80) cc_final: 0.7819 (t80)
REVERT: A  206 ILE cc_start: 0.8820 (mp) cc_final: 0.8607 (tp)
REVERT: A  222 LEU cc_start: 0.7888 (mt) cc_final: 0.7608 (pt)
REVERT: A  229 ASN cc_start: 0.8830 (t0) cc_final: 0.8575 (t0)
REVERT: A  258 ILE cc_start: 0.7717 (tt) cc_final: 0.7419 (tt)
REVERT: A  260 MET cc_start: 0.6229 (tpt) cc_final: 0.6010 (tpp)
REVERT: A  297 CYS cc_start: 0.5580 (m) cc_final: 0.5318 (m)
REVERT: A  323 GLU cc_start: 0.8572 (tt0) cc_final: 0.8192 (tm-30)
REVERT: A  365 LEU cc_start: 0.8692 (mt) cc_final: 0.7848 (mt)
REVERT: A  382 LEU cc_start: 0.8436 (mt) cc_final: 0.7941 (mt)
REVERT: A  397 MET cc_start: 0.8397 (mtm) cc_final: 0.7947 (mtt)
REVERT: A  441 ASP cc_start: 0.9003 (m-30) cc_final: 0.8591 (p0)
REVERT: A  528 TYR cc_start: 0.7055 (t80) cc_final: 0.6800 (t80)
REVERT: A  617 MET cc_start: 0.8245 (mmm) cc_final: 0.7719 (mmt)
REVERT: A  650 ILE cc_start: 0.7987 (pt) cc_final: 0.7777 (pt)
REVERT: B   20 LEU cc_start: 0.9132 (tp) cc_final: 0.8764 (tp)
REVERT: B  155 PHE cc_start: 0.6400 (t80) cc_final: 0.6073 (t80)
REVERT: B  524 GLU cc_start: 0.7783 (pt0) cc_final: 0.6198 (mm-30)
REVERT: B  529 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8410 (tm-30)
REVERT: B  533 ASP cc_start: 0.7930 (m-30) cc_final: 0.7672 (m-30)
REVERT: B  552 LEU cc_start: 0.8632 (mm) cc_final: 0.8371 (mm)
REVERT: B  554 VAL cc_start: 0.8963 (t) cc_final: 0.8756 (t)
REVERT: B  602 ASN cc_start: 0.7865 (m-40) cc_final: 0.7663 (p0)
REVERT: B  644 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7273 (tptt)
REVERT: B  692 MET cc_start: 0.5877 (ttm) cc_final: 0.4890 (ttm)
REVERT: B  759 MET cc_start: 0.8459 (mmp) cc_final: 0.8180 (mmp)
REVERT: B  795 GLU cc_start: 0.8830 (pt0) cc_final: 0.8568 (pp20)
  outliers start: 5
  outliers final: 2
  residues processed: 273
  average time/residue: 0.4034
  time to fit residues: 143.0291
Evaluate side-chains
  202 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 136 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 134 optimal weight:    6.9990
   chunk 111 optimal weight:    0.0770
   chunk 56 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    5.8146

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS
A 326 GLN
A 339 GLN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
B 683 ASN
** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.073735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.064801 restraints weight = 70720.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.066334 restraints weight = 50676.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.067464 restraints weight = 38057.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.5254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10976  Z= 0.194
  Angle     :  0.739   9.301  14869  Z= 0.374
  Chirality :  0.045   0.168   1706
  Planarity :  0.006   0.080   1934
  Dihedral  :  7.152 121.343   1532
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.61 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.21), residues: 1355
  helix:  1.28 (0.19), residues: 662
  sheet: -0.44 (0.34), residues: 185
  loop : -0.87 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 709 
 HIS   0.010   0.001   HIS B 370 
 PHE   0.019   0.002   PHE B 334 
 TYR   0.032   0.003   TYR B  31 
 ARG   0.017   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  552)
  hydrogen bonds       : angle       5.00924 ( 1557)
  covalent geometry    : bond        0.00421 (10976)
  covalent geometry    : angle       0.73912 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 243
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7959 (mmm160)
REVERT: A   40 PHE cc_start: 0.6388 (m-10) cc_final: 0.6153 (m-80)
REVERT: A  143 PHE cc_start: 0.6280 (m-80) cc_final: 0.5946 (m-80)
REVERT: A  222 LEU cc_start: 0.8088 (mt) cc_final: 0.7704 (pt)
REVERT: A  229 ASN cc_start: 0.9042 (t0) cc_final: 0.8718 (t0)
REVERT: A  260 MET cc_start: 0.6470 (tpt) cc_final: 0.6224 (tpp)
REVERT: A  323 GLU cc_start: 0.8456 (tt0) cc_final: 0.8070 (tm-30)
REVERT: A  397 MET cc_start: 0.8455 (mtm) cc_final: 0.7907 (mtt)
REVERT: A  441 ASP cc_start: 0.8948 (m-30) cc_final: 0.8665 (p0)
REVERT: A  528 TYR cc_start: 0.7112 (t80) cc_final: 0.6891 (t80)
REVERT: A  552 LEU cc_start: 0.8895 (mt) cc_final: 0.8685 (mp)
REVERT: A  615 PRO cc_start: 0.7302 (Cg_endo) cc_final: 0.5658 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8339 (mmm) cc_final: 0.7907 (mmm)
REVERT: B  124 LEU cc_start: 0.7331 (mt) cc_final: 0.7109 (mt)
REVERT: B  174 ASN cc_start: 0.8688 (t0) cc_final: 0.8213 (t0)
REVERT: B  289 ASN cc_start: 0.8703 (t0) cc_final: 0.8326 (t0)
REVERT: B  529 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8299 (tm-30)
REVERT: B  533 ASP cc_start: 0.7776 (m-30) cc_final: 0.7453 (m-30)
REVERT: B  552 LEU cc_start: 0.8776 (mm) cc_final: 0.8551 (mm)
REVERT: B  554 VAL cc_start: 0.8997 (t) cc_final: 0.8782 (p)
REVERT: B  654 PHE cc_start: 0.4707 (m-80) cc_final: 0.4328 (m-80)
REVERT: B  692 MET cc_start: 0.5841 (ttm) cc_final: 0.4725 (ttm)
REVERT: B  724 LEU cc_start: 0.8975 (mt) cc_final: 0.8773 (mt)
REVERT: B  759 MET cc_start: 0.8420 (mmp) cc_final: 0.8150 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 246
  average time/residue: 0.2859
  time to fit residues: 93.5896
Evaluate side-chains
  193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 126 optimal weight:   30.0000
   chunk 117 optimal weight:   10.0000
   chunk 44 optimal weight:   30.0000
   chunk 135 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 118 optimal weight:    4.9990
   chunk 134 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.072998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.064046 restraints weight = 70231.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.065538 restraints weight = 50329.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.066650 restraints weight = 37916.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.5794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10976  Z= 0.176
  Angle     :  0.729   9.943  14869  Z= 0.373
  Chirality :  0.044   0.185   1706
  Planarity :  0.005   0.054   1934
  Dihedral  :  7.012 120.972   1532
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.87 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.21), residues: 1355
  helix:  1.28 (0.19), residues: 657
  sheet: -0.38 (0.37), residues: 162
  loop : -0.92 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 709 
 HIS   0.006   0.001   HIS A 312 
 PHE   0.022   0.002   PHE A 670 
 TYR   0.024   0.002   TYR B  31 
 ARG   0.008   0.001   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  552)
  hydrogen bonds       : angle       5.01427 ( 1557)
  covalent geometry    : bond        0.00388 (10976)
  covalent geometry    : angle       0.72877 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 220
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.6254 (m-10) cc_final: 0.6038 (m-80)
REVERT: A  143 PHE cc_start: 0.6412 (m-80) cc_final: 0.5921 (m-80)
REVERT: A  170 LEU cc_start: 0.7601 (mt) cc_final: 0.7296 (mt)
REVERT: A  207 ASP cc_start: 0.8933 (m-30) cc_final: 0.8724 (m-30)
REVERT: A  222 LEU cc_start: 0.8068 (mt) cc_final: 0.7660 (pt)
REVERT: A  229 ASN cc_start: 0.9088 (t0) cc_final: 0.8699 (t0)
REVERT: A  323 GLU cc_start: 0.8295 (tt0) cc_final: 0.8085 (tm-30)
REVERT: A  365 LEU cc_start: 0.8238 (mt) cc_final: 0.7725 (mt)
REVERT: A  397 MET cc_start: 0.8417 (mtm) cc_final: 0.7755 (mtt)
REVERT: A  441 ASP cc_start: 0.9015 (m-30) cc_final: 0.8590 (p0)
REVERT: A  528 TYR cc_start: 0.7202 (t80) cc_final: 0.6921 (t80)
REVERT: A  552 LEU cc_start: 0.8873 (mt) cc_final: 0.8655 (mp)
REVERT: A  615 PRO cc_start: 0.7317 (Cg_endo) cc_final: 0.6002 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8191 (mmm) cc_final: 0.7826 (mmm)
REVERT: A  692 MET cc_start: 0.7943 (mmp) cc_final: 0.7691 (mmp)
REVERT: B   49 GLN cc_start: 0.4576 (OUTLIER) cc_final: 0.3860 (pm20)
REVERT: B  124 LEU cc_start: 0.7458 (mt) cc_final: 0.7130 (mt)
REVERT: B  155 PHE cc_start: 0.6638 (t80) cc_final: 0.6434 (t80)
REVERT: B  386 ASP cc_start: 0.7807 (p0) cc_final: 0.7605 (p0)
REVERT: B  529 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8310 (tm-30)
REVERT: B  533 ASP cc_start: 0.7758 (m-30) cc_final: 0.7386 (m-30)
REVERT: B  552 LEU cc_start: 0.8808 (mm) cc_final: 0.8597 (mm)
REVERT: B  717 ASN cc_start: 0.8305 (t0) cc_final: 0.7989 (t0)
REVERT: B  759 MET cc_start: 0.8426 (mmp) cc_final: 0.8166 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2727
  time to fit residues: 81.7252
Evaluate side-chains
  183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   chunk 83 optimal weight:    8.9990
   chunk 101 optimal weight:    9.9990
   chunk 121 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 122 optimal weight:    0.9980
   chunk 133 optimal weight:    0.3980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 746 HIS
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.073879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.064925 restraints weight = 69989.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.066449 restraints weight = 50080.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.067565 restraints weight = 37673.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.6053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10976  Z= 0.140
  Angle     :  0.689   8.482  14869  Z= 0.345
  Chirality :  0.042   0.188   1706
  Planarity :  0.005   0.053   1934
  Dihedral  :  6.689 119.683   1532
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.22), residues: 1355
  helix:  1.44 (0.19), residues: 659
  sheet: -0.28 (0.38), residues: 166
  loop : -0.93 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 709 
 HIS   0.005   0.001   HIS A 312 
 PHE   0.013   0.001   PHE B 372 
 TYR   0.019   0.002   TYR A 635 
 ARG   0.008   0.001   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  552)
  hydrogen bonds       : angle       4.89555 ( 1557)
  covalent geometry    : bond        0.00306 (10976)
  covalent geometry    : angle       0.68913 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.7040 (mtm) cc_final: 0.6802 (mtt)
REVERT: A  143 PHE cc_start: 0.6046 (m-80) cc_final: 0.5755 (m-80)
REVERT: A  166 MET cc_start: 0.6382 (tpt) cc_final: 0.6011 (tpt)
REVERT: A  170 LEU cc_start: 0.7398 (mt) cc_final: 0.7117 (mt)
REVERT: A  222 LEU cc_start: 0.8221 (mt) cc_final: 0.7798 (pt)
REVERT: A  229 ASN cc_start: 0.9031 (t0) cc_final: 0.8596 (t0)
REVERT: A  397 MET cc_start: 0.8417 (mtm) cc_final: 0.7723 (mtt)
REVERT: A  432 GLU cc_start: 0.8620 (tt0) cc_final: 0.8031 (tp30)
REVERT: A  441 ASP cc_start: 0.9025 (m-30) cc_final: 0.8571 (p0)
REVERT: A  528 TYR cc_start: 0.7147 (t80) cc_final: 0.6839 (t80)
REVERT: A  615 PRO cc_start: 0.7218 (Cg_endo) cc_final: 0.5892 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8117 (mmm) cc_final: 0.7758 (mmm)
REVERT: A  674 MET cc_start: 0.7975 (tmm) cc_final: 0.7774 (tmm)
REVERT: B  529 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8210 (tm-30)
REVERT: B  533 ASP cc_start: 0.7806 (m-30) cc_final: 0.7457 (m-30)
REVERT: B  552 LEU cc_start: 0.8767 (mm) cc_final: 0.8550 (mm)
REVERT: B  624 MET cc_start: 0.8570 (tmm) cc_final: 0.7987 (mtp)
REVERT: B  705 LEU cc_start: 0.7404 (tp) cc_final: 0.7194 (tp)
REVERT: B  717 ASN cc_start: 0.8346 (t0) cc_final: 0.7694 (t0)
REVERT: B  725 PHE cc_start: 0.6746 (m-80) cc_final: 0.5880 (m-10)
REVERT: B  739 MET cc_start: 0.6376 (ttt) cc_final: 0.6149 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2854
  time to fit residues: 82.9202
Evaluate side-chains
  180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 115 optimal weight:   30.0000
   chunk 72 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 129 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 ASN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 734 GLN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.072571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.063886 restraints weight = 76807.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.065221 restraints weight = 56766.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.066266 restraints weight = 43853.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.6503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10976  Z= 0.183
  Angle     :  0.733   9.359  14869  Z= 0.370
  Chirality :  0.044   0.175   1706
  Planarity :  0.006   0.125   1934
  Dihedral  :  6.644 118.699   1532
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.29 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.46 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.22), residues: 1355
  helix:  1.21 (0.19), residues: 661
  sheet: -0.31 (0.40), residues: 154
  loop : -0.96 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 709 
 HIS   0.005   0.001   HIS A 312 
 PHE   0.024   0.002   PHE B 155 
 TYR   0.040   0.002   TYR B  31 
 ARG   0.015   0.001   ARG B 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  552)
  hydrogen bonds       : angle       4.96122 ( 1557)
  covalent geometry    : bond        0.00401 (10976)
  covalent geometry    : angle       0.73289 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.7069 (mtm) cc_final: 0.6772 (mtt)
REVERT: A   40 PHE cc_start: 0.6415 (m-10) cc_final: 0.6166 (m-80)
REVERT: A  143 PHE cc_start: 0.6253 (m-80) cc_final: 0.5969 (m-80)
REVERT: A  166 MET cc_start: 0.6089 (tpt) cc_final: 0.5827 (tpt)
REVERT: A  170 LEU cc_start: 0.7549 (mt) cc_final: 0.7275 (mt)
REVERT: A  205 GLU cc_start: 0.8422 (tp30) cc_final: 0.8187 (mm-30)
REVERT: A  222 LEU cc_start: 0.8086 (mt) cc_final: 0.7716 (pt)
REVERT: A  229 ASN cc_start: 0.9076 (t0) cc_final: 0.8632 (t0)
REVERT: A  397 MET cc_start: 0.8317 (mtm) cc_final: 0.7698 (mtt)
REVERT: A  432 GLU cc_start: 0.8654 (tt0) cc_final: 0.7923 (tp30)
REVERT: A  441 ASP cc_start: 0.9033 (m-30) cc_final: 0.8642 (p0)
REVERT: A  615 PRO cc_start: 0.7389 (Cg_endo) cc_final: 0.6155 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8066 (mmm) cc_final: 0.7788 (mmm)
REVERT: A  674 MET cc_start: 0.8157 (tmm) cc_final: 0.7939 (tmm)
REVERT: A  692 MET cc_start: 0.7702 (mmp) cc_final: 0.7481 (mtt)
REVERT: B  155 PHE cc_start: 0.6691 (t80) cc_final: 0.6462 (t80)
REVERT: B  386 ASP cc_start: 0.7552 (p0) cc_final: 0.7348 (p0)
REVERT: B  529 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8285 (tm-30)
REVERT: B  533 ASP cc_start: 0.7815 (m-30) cc_final: 0.7467 (m-30)
REVERT: B  609 MET cc_start: 0.7938 (ttt) cc_final: 0.7322 (ttt)
REVERT: B  717 ASN cc_start: 0.8286 (t0) cc_final: 0.7377 (t0)
REVERT: B  739 MET cc_start: 0.6531 (ttt) cc_final: 0.5968 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2697
  time to fit residues: 75.4174
Evaluate side-chains
  168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 126 optimal weight:   20.0000
   chunk 82 optimal weight:   30.0000
   chunk 15 optimal weight:    6.9990
   chunk 134 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 119 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 GLN
B 131 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.070675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.062087 restraints weight = 78276.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.063439 restraints weight = 57796.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.064458 restraints weight = 44477.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.6950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10976  Z= 0.209
  Angle     :  0.765   7.406  14869  Z= 0.390
  Chirality :  0.045   0.203   1706
  Planarity :  0.006   0.046   1934
  Dihedral  :  6.750 120.107   1532
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 21.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.67 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.22), residues: 1355
  helix:  0.99 (0.19), residues: 657
  sheet: -0.55 (0.40), residues: 162
  loop : -1.08 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 709 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.020   0.002   PHE B 670 
 TYR   0.027   0.002   TYR B  31 
 ARG   0.008   0.001   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  552)
  hydrogen bonds       : angle       5.10426 ( 1557)
  covalent geometry    : bond        0.00458 (10976)
  covalent geometry    : angle       0.76534 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 1.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.7182 (mtm) cc_final: 0.6820 (mtt)
REVERT: A   28 LEU cc_start: 0.8284 (tp) cc_final: 0.7989 (tp)
REVERT: A  133 LEU cc_start: 0.8038 (tp) cc_final: 0.7745 (tp)
REVERT: A  143 PHE cc_start: 0.6299 (m-80) cc_final: 0.5949 (m-80)
REVERT: A  205 GLU cc_start: 0.8474 (tp30) cc_final: 0.8243 (mm-30)
REVERT: A  222 LEU cc_start: 0.8212 (mt) cc_final: 0.7827 (pt)
REVERT: A  229 ASN cc_start: 0.9053 (t0) cc_final: 0.8729 (t0)
REVERT: A  397 MET cc_start: 0.8359 (mtm) cc_final: 0.7719 (mtt)
REVERT: A  432 GLU cc_start: 0.8631 (tt0) cc_final: 0.7921 (tp30)
REVERT: A  441 ASP cc_start: 0.9022 (m-30) cc_final: 0.8615 (p0)
REVERT: A  615 PRO cc_start: 0.7518 (Cg_endo) cc_final: 0.6292 (Cg_exo)
REVERT: A  692 MET cc_start: 0.7724 (mmp) cc_final: 0.7322 (mtp)
REVERT: B   73 TYR cc_start: 0.6857 (p90) cc_final: 0.6336 (p90)
REVERT: B  155 PHE cc_start: 0.6862 (t80) cc_final: 0.6621 (t80)
REVERT: B  269 MET cc_start: 0.8450 (ttp) cc_final: 0.8222 (ttm)
REVERT: B  386 ASP cc_start: 0.7587 (p0) cc_final: 0.7290 (p0)
REVERT: B  529 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8422 (tm-30)
REVERT: B  533 ASP cc_start: 0.7832 (m-30) cc_final: 0.7477 (m-30)
REVERT: B  552 LEU cc_start: 0.8785 (mm) cc_final: 0.8565 (mm)
REVERT: B  624 MET cc_start: 0.8498 (tmm) cc_final: 0.7917 (mtp)
REVERT: B  739 MET cc_start: 0.6838 (ttt) cc_final: 0.6216 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2762
  time to fit residues: 74.2115
Evaluate side-chains
  168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 127 optimal weight:    8.9990
   chunk 126 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 131 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
A 626 GLN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN
B 734 GLN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.069536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.061043 restraints weight = 71426.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.062454 restraints weight = 51310.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.063510 restraints weight = 38734.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.7253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10976  Z= 0.190
  Angle     :  0.759  10.401  14869  Z= 0.385
  Chirality :  0.045   0.180   1706
  Planarity :  0.005   0.048   1934
  Dihedral  :  6.744 121.396   1532
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.50 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1355
  helix:  1.06 (0.20), residues: 650
  sheet: -0.58 (0.40), residues: 163
  loop : -1.14 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B 709 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.019   0.002   PHE B 155 
 TYR   0.024   0.002   TYR A 635 
 ARG   0.013   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  552)
  hydrogen bonds       : angle       5.12134 ( 1557)
  covalent geometry    : bond        0.00423 (10976)
  covalent geometry    : angle       0.75928 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.7090 (mtm) cc_final: 0.6810 (mtt)
REVERT: A   28 LEU cc_start: 0.8266 (tp) cc_final: 0.7991 (tp)
REVERT: A  143 PHE cc_start: 0.6479 (m-80) cc_final: 0.6165 (m-10)
REVERT: A  166 MET cc_start: 0.6281 (tpt) cc_final: 0.6057 (tpt)
REVERT: A  170 LEU cc_start: 0.7528 (mt) cc_final: 0.7157 (mt)
REVERT: A  222 LEU cc_start: 0.8348 (mt) cc_final: 0.7974 (pt)
REVERT: A  229 ASN cc_start: 0.9097 (t0) cc_final: 0.8800 (t0)
REVERT: A  397 MET cc_start: 0.8165 (mtm) cc_final: 0.7585 (mtt)
REVERT: A  409 ARG cc_start: 0.7204 (ptt-90) cc_final: 0.6837 (mtm110)
REVERT: A  432 GLU cc_start: 0.8608 (tt0) cc_final: 0.7915 (tp30)
REVERT: A  441 ASP cc_start: 0.8995 (m-30) cc_final: 0.8575 (p0)
REVERT: A  615 PRO cc_start: 0.7533 (Cg_endo) cc_final: 0.6388 (Cg_exo)
REVERT: A  692 MET cc_start: 0.7733 (mmp) cc_final: 0.7118 (mtp)
REVERT: B   17 TYR cc_start: 0.3972 (t80) cc_final: 0.3282 (t80)
REVERT: B   73 TYR cc_start: 0.6903 (p90) cc_final: 0.6365 (p90)
REVERT: B  155 PHE cc_start: 0.6753 (t80) cc_final: 0.6034 (t80)
REVERT: B  258 ILE cc_start: 0.9130 (tt) cc_final: 0.8601 (tt)
REVERT: B  269 MET cc_start: 0.8420 (ttp) cc_final: 0.8196 (ttm)
REVERT: B  386 ASP cc_start: 0.7555 (p0) cc_final: 0.7259 (p0)
REVERT: B  529 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8372 (tm-30)
REVERT: B  533 ASP cc_start: 0.7813 (m-30) cc_final: 0.7482 (m-30)
REVERT: B  609 MET cc_start: 0.8261 (tpt) cc_final: 0.7859 (tpt)
REVERT: B  717 ASN cc_start: 0.8022 (t0) cc_final: 0.7201 (t0)
REVERT: B  739 MET cc_start: 0.7064 (ttt) cc_final: 0.6418 (ttt)
  outliers start: 1
  outliers final: 1
  residues processed: 191
  average time/residue: 0.2862
  time to fit residues: 74.4197
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 135 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   chunk 120 optimal weight:    9.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.070174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.061855 restraints weight = 77831.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.063156 restraints weight = 57344.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.064158 restraints weight = 44279.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.7451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10976  Z= 0.174
  Angle     :  0.756  11.893  14869  Z= 0.381
  Chirality :  0.045   0.207   1706
  Planarity :  0.005   0.051   1934
  Dihedral  :  6.669 121.365   1532
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 20.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1355
  helix:  1.09 (0.20), residues: 650
  sheet: -0.48 (0.41), residues: 155
  loop : -1.25 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 137 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.015   0.002   PHE B 155 
 TYR   0.031   0.002   TYR A 635 
 ARG   0.011   0.001   ARG A 343 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  552)
  hydrogen bonds       : angle       5.09960 ( 1557)
  covalent geometry    : bond        0.00393 (10976)
  covalent geometry    : angle       0.75555 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.6974 (mtm) cc_final: 0.6627 (mtt)
REVERT: A  143 PHE cc_start: 0.6293 (m-80) cc_final: 0.6046 (m-10)
REVERT: A  166 MET cc_start: 0.6268 (tpt) cc_final: 0.5772 (tpt)
REVERT: A  222 LEU cc_start: 0.8390 (mt) cc_final: 0.8017 (pt)
REVERT: A  229 ASN cc_start: 0.9136 (t0) cc_final: 0.8795 (t0)
REVERT: A  432 GLU cc_start: 0.8637 (tt0) cc_final: 0.7956 (tp30)
REVERT: A  441 ASP cc_start: 0.9029 (m-30) cc_final: 0.8587 (p0)
REVERT: A  615 PRO cc_start: 0.7561 (Cg_endo) cc_final: 0.6427 (Cg_exo)
REVERT: A  692 MET cc_start: 0.7771 (mmp) cc_final: 0.7067 (mtp)
REVERT: B   73 TYR cc_start: 0.6965 (p90) cc_final: 0.6433 (p90)
REVERT: B  258 ILE cc_start: 0.9094 (tt) cc_final: 0.8856 (tt)
REVERT: B  386 ASP cc_start: 0.7408 (p0) cc_final: 0.7060 (p0)
REVERT: B  529 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8367 (tm-30)
REVERT: B  533 ASP cc_start: 0.7830 (m-30) cc_final: 0.7502 (m-30)
REVERT: B  644 LYS cc_start: 0.8741 (tttm) cc_final: 0.8453 (tptt)
REVERT: B  705 LEU cc_start: 0.7594 (tp) cc_final: 0.7336 (tp)
REVERT: B  717 ASN cc_start: 0.8016 (t0) cc_final: 0.7323 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2701
  time to fit residues: 70.7687
Evaluate side-chains
  151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 40 optimal weight:   30.0000
   chunk 136 optimal weight:   20.0000
   chunk 123 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 752 HIS
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.069252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.061267 restraints weight = 72800.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.062515 restraints weight = 54016.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.063467 restraints weight = 41820.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.7707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10976  Z= 0.197
  Angle     :  0.804  12.665  14869  Z= 0.405
  Chirality :  0.045   0.215   1706
  Planarity :  0.006   0.057   1934
  Dihedral  :  6.717 121.897   1532
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 22.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.21), residues: 1355
  helix:  0.94 (0.20), residues: 650
  sheet: -0.45 (0.41), residues: 155
  loop : -1.31 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 709 
 HIS   0.008   0.001   HIS A 312 
 PHE   0.047   0.003   PHE B 730 
 TYR   0.031   0.003   TYR A 635 
 ARG   0.012   0.001   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  552)
  hydrogen bonds       : angle       5.25025 ( 1557)
  covalent geometry    : bond        0.00440 (10976)
  covalent geometry    : angle       0.80446 (14869)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.7020 (mtm) cc_final: 0.6770 (mtt)
REVERT: A  143 PHE cc_start: 0.6379 (m-80) cc_final: 0.6044 (m-10)
REVERT: A  166 MET cc_start: 0.6231 (tpt) cc_final: 0.5728 (tpt)
REVERT: A  222 LEU cc_start: 0.8394 (mt) cc_final: 0.8084 (pt)
REVERT: A  229 ASN cc_start: 0.9111 (t0) cc_final: 0.8789 (t0)
REVERT: A  397 MET cc_start: 0.8042 (mtm) cc_final: 0.7484 (mtt)
REVERT: A  432 GLU cc_start: 0.8629 (tt0) cc_final: 0.7907 (tp30)
REVERT: A  441 ASP cc_start: 0.8985 (m-30) cc_final: 0.8536 (p0)
REVERT: A  615 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.6432 (Cg_exo)
REVERT: A  626 GLN cc_start: 0.7837 (tt0) cc_final: 0.7538 (tt0)
REVERT: A  692 MET cc_start: 0.7719 (mmp) cc_final: 0.7438 (mmp)
REVERT: B   73 TYR cc_start: 0.6944 (p90) cc_final: 0.6397 (p90)
REVERT: B  155 PHE cc_start: 0.6716 (t80) cc_final: 0.6148 (t80)
REVERT: B  187 MET cc_start: 0.4802 (mmm) cc_final: 0.4338 (mmm)
REVERT: B  258 ILE cc_start: 0.9206 (tt) cc_final: 0.8516 (tt)
REVERT: B  386 ASP cc_start: 0.7194 (p0) cc_final: 0.6848 (p0)
REVERT: B  644 LYS cc_start: 0.8722 (tttm) cc_final: 0.8388 (tptt)
REVERT: B  705 LEU cc_start: 0.7620 (tp) cc_final: 0.7329 (tp)
REVERT: B  717 ASN cc_start: 0.8021 (t0) cc_final: 0.7389 (t0)
REVERT: B  739 MET cc_start: 0.6627 (ttt) cc_final: 0.6320 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2845
  time to fit residues: 73.6021
Evaluate side-chains
  157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 11 optimal weight:    0.3980
   chunk 118 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 94 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 752 HIS
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.071009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.062710 restraints weight = 76461.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.063997 restraints weight = 56767.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.064972 restraints weight = 44006.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.7785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10976  Z= 0.158
  Angle     :  0.779  12.569  14869  Z= 0.388
  Chirality :  0.045   0.217   1706
  Planarity :  0.005   0.058   1934
  Dihedral  :  6.548 121.086   1532
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 19.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.22), residues: 1355
  helix:  1.25 (0.20), residues: 638
  sheet: -0.47 (0.36), residues: 192
  loop : -1.10 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B 709 
 HIS   0.007   0.001   HIS A 312 
 PHE   0.055   0.002   PHE A 670 
 TYR   0.028   0.002   TYR A 635 
 ARG   0.013   0.001   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  552)
  hydrogen bonds       : angle       5.13557 ( 1557)
  covalent geometry    : bond        0.00360 (10976)
  covalent geometry    : angle       0.77871 (14869)

===============================================================================
Job complete
usr+sys time: 3467.98 seconds
wall clock time: 62 minutes 15.14 seconds (3735.14 seconds total)