Starting phenix.real_space_refine
on Wed Aug  5 01:30:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oeg_70398/08_2026/9oeg_70398.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4954      2.51       5
     N    1330      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7796
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "K"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 814
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 2138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2138
          Classifications: {'peptide': 270}
          Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 253}
          Chain breaks: 1
  Restraints were copied for chains:
    J, L, B
  Time building chain proxies: 1.96, per 1000 atoms: 0.25
  Number of scatterers: 7796
  At special positions: 0
  Unit cell: (116.387, 87.4907, 73.8453, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1476      8.00
     N    1330      7.00
     C    4954      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 456.8 milliseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1796

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 20 sheets defined
      3.4% alpha, 54.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'K' and resid 79 through 83
      removed outlier: 4.118A  pdb=" N   PHE K  83 " --> pdb=" O   SER K  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.119A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 664
    Processing helix  chain 'B' and resid 658 through 664
    Processing helix  chain 'J' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.819A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.060A  pdb=" N   PHE H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 7
      removed outlier: 6.293A  pdb=" N   THR K  69 " --> pdb=" O   ALA K  25 " (cutoff:3.500A)
      removed outlier: 10.298A  pdb=" N   GLU K  27 " --> pdb=" O   SER K  67 " (cutoff:3.500A)
      removed outlier: 10.105A  pdb=" N   SER K  67 " --> pdb=" O   GLU K  27 " (cutoff:3.500A)
      removed outlier: 11.772A  pdb=" N   ILE K  29 " --> pdb=" O   SER K  65 " (cutoff:3.500A)
      removed outlier: 11.783A  pdb=" N   SER K  65 " --> pdb=" O   ILE K  29 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 10 through 12
      removed outlier: 3.740A  pdb=" N   VAL K  48 " --> pdb=" O   TRP K  35 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLN K  37 " --> pdb=" O   LEU K  46 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   LEU K  46 " --> pdb=" O   GLN K  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
      removed outlier: 6.293A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.298A  pdb=" N   GLU L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 10.106A  pdb=" N   SER L  67 " --> pdb=" O   GLU L  27 " (cutoff:3.500A)
      removed outlier: 11.771A  pdb=" N   ILE L  29 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 11.783A  pdb=" N   SER L  65 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.739A  pdb=" N   VAL L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 476
      removed outlier: 6.513A  pdb=" N   VAL A 466 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA A 475 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   PHE A 464 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 513 " --> pdb=" O   GLY A 524 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLY A 524 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG A 520 " --> pdb=" O   GLN A 517 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL A 528 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS A 556 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL A 489 " --> pdb=" O   TRP A 500 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   TRP A 500 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   THR A 491 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A 496 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 476
      removed outlier: 6.513A  pdb=" N   VAL A 466 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA A 475 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   PHE A 464 " --> pdb=" O   ALA A 475 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 513 " --> pdb=" O   GLY A 524 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLY A 524 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG A 520 " --> pdb=" O   GLN A 517 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL A 528 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS A 556 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A 671 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 445 through 446
      removed outlier: 4.423A  pdb=" N   GLN A 570 " --> pdb=" O   PHE A 597 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 445 through 446
      removed outlier: 4.423A  pdb=" N   GLN A 570 " --> pdb=" O   PHE A 597 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   SER B 585 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   THR A 596 " --> pdb=" O   SER B 585 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 567 through 568
    Processing sheet with id=AB4, first strand: chain 'A' and resid 584 through 585
      removed outlier: 4.422A  pdb=" N   GLN B 570 " --> pdb=" O   PHE B 597 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 584 through 585
    Processing sheet with id=AB6, first strand: chain 'B' and resid 471 through 476
      removed outlier: 6.513A  pdb=" N   VAL B 466 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA B 475 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   PHE B 464 " --> pdb=" O   ALA B 475 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL B 513 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG B 520 " --> pdb=" O   GLN B 517 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL B 528 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   LYS B 556 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL B 489 " --> pdb=" O   TRP B 500 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   TRP B 500 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   THR B 491 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS B 496 " --> pdb=" O   ASP B 493 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 471 through 476
      removed outlier: 6.513A  pdb=" N   VAL B 466 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA B 475 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   PHE B 464 " --> pdb=" O   ALA B 475 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL B 513 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG B 520 " --> pdb=" O   GLN B 517 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL B 528 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   LYS B 556 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP B 671 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 567 through 568
    Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7
    Processing sheet with id=AC1, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.819A  pdb=" N   MET J  34 " --> pdb=" O   TYR J  50 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   TYR J  50 " --> pdb=" O   MET J  34 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP J  36 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12
      removed outlier: 4.060A  pdb=" N   PHE J 102 " --> pdb=" O   ARG J  94 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    840 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: 1.37

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2504
        1.34 -     1.46: 2051
        1.46 -     1.58: 3399
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 8014
  Sorted by residual:
  bond pdb=" N   ASN A 469 "
       pdb=" CA  ASN A 469 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.010 1.29e-02 6.01e+03 6.60e-01
  bond pdb=" N   ILE A 522 "
       pdb=" CA  ILE A 522 "
    ideal  model  delta    sigma   weight residual
    1.462  1.473 -0.011 1.32e-02 5.74e+03 6.35e-01
  bond pdb=" N   ILE B 522 "
       pdb=" CA  ILE B 522 "
    ideal  model  delta    sigma   weight residual
    1.462  1.473 -0.011 1.32e-02 5.74e+03 6.35e-01
  bond pdb=" CA  ASN A 469 "
       pdb=" C   ASN A 469 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.010 1.34e-02 5.57e+03 6.13e-01
  bond pdb=" N   SER L  31 "
       pdb=" CA  SER L  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.465 -0.007 9.00e-03 1.23e+04 5.89e-01
  ... (remaining 8009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 10220
        1.01 -     2.01: 552
        2.01 -     3.02: 104
        3.02 -     4.02: 28
        4.02 -     5.03: 8
  Bond angle restraints: 10912
  Sorted by residual:
  angle pdb=" N   VAL A 473 "
        pdb=" CA  VAL A 473 "
        pdb=" C   VAL A 473 "
      ideal   model   delta    sigma   weight residual
     111.58  109.12    2.46 1.06e+00 8.90e-01 5.40e+00
  angle pdb=" N   VAL B 473 "
        pdb=" CA  VAL B 473 "
        pdb=" C   VAL B 473 "
      ideal   model   delta    sigma   weight residual
     111.58  109.13    2.45 1.06e+00 8.90e-01 5.33e+00
  angle pdb=" C   ASN B 469 "
        pdb=" N   ASN B 470 "
        pdb=" CA  ASN B 470 "
      ideal   model   delta    sigma   weight residual
     121.70  125.77   -4.07 1.80e+00 3.09e-01 5.10e+00
  angle pdb=" C   ASN A 469 "
        pdb=" N   ASN A 470 "
        pdb=" CA  ASN A 470 "
      ideal   model   delta    sigma   weight residual
     121.70  125.73   -4.03 1.80e+00 3.09e-01 5.02e+00
  angle pdb=" N   ALA K  50 "
        pdb=" CA  ALA K  50 "
        pdb=" C   ALA K  50 "
      ideal   model   delta    sigma   weight residual
     112.86  110.33    2.53 1.22e+00 6.72e-01 4.30e+00
  ... (remaining 10907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4388
       16.07 -    32.14: 186
       32.14 -    48.21: 26
       48.21 -    64.27: 10
       64.27 -    80.34: 6
  Dihedral angle restraints: 4616
    sinusoidal: 1790
      harmonic: 2826
  Sorted by residual:
  dihedral pdb=" CA  HIS H  35 "
           pdb=" C   HIS H  35 "
           pdb=" N   TRP H  36 "
           pdb=" CA  TRP H  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.04   15.96     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  HIS J  35 "
           pdb=" C   HIS J  35 "
           pdb=" N   TRP J  36 "
           pdb=" CA  TRP J  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.07   15.93     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" N   GLN J  81 "
           pdb=" CA  GLN J  81 "
           pdb=" CB  GLN J  81 "
           pdb=" CG  GLN J  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.75   58.75     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 4613 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 700
       0.026 -    0.053: 291
       0.053 -    0.079: 76
       0.079 -    0.106: 73
       0.106 -    0.132: 32
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  ILE L  21 "
            pdb=" N   ILE L  21 "
            pdb=" C   ILE L  21 "
            pdb=" CB  ILE L  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE K  21 "
            pdb=" N   ILE K  21 "
            pdb=" C   ILE K  21 "
            pdb=" CB  ILE K  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE J  57 "
            pdb=" N   ILE J  57 "
            pdb=" C   ILE J  57 "
            pdb=" CB  ILE J  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1169 not shown)

  Planarity restraints: 1394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 648 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO A 649 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 649 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 649 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 648 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO B 649 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 649 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 649 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 572 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.57e-01
        pdb=" N   PRO B 573 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO B 573 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 573 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1391 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.04: 4418
        3.04 -     3.51: 7355
        3.51 -     3.97: 12740
        3.97 -     4.44: 15421
        4.44 -     4.90: 25624
  Nonbonded interactions: 65558
  Sorted by model distance:
  nonbonded pdb=" N   THR B 449 "
            pdb=" OG1 THR B 449 "
     model   vdw
     2.580 2.496
  nonbonded pdb=" N   THR A 449 "
            pdb=" OG1 THR A 449 "
     model   vdw
     2.580 2.496
  nonbonded pdb=" N   ASN B 470 "
            pdb=" N   THR B 471 "
     model   vdw
     2.605 2.560
  nonbonded pdb=" N   ASN A 470 "
            pdb=" N   THR A 471 "
     model   vdw
     2.606 2.560
  nonbonded pdb=" N   LEU B 574 "
            pdb=" O   LEU B 574 "
     model   vdw
     2.630 2.496
  ... (remaining 65553 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.610
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
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      :  0.002   0.015   8018  Z= 0.114
  Angle     :  0.544   5.025  10920  Z= 0.314
  Chirality :  0.041   0.132   1172
  Planarity :  0.003   0.030   1394
  Dihedral  : 10.121  80.342   2808
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  4.29 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.26), residues: 976
  helix: -0.93 (1.59), residues: 12
  sheet:  0.08 (0.26), residues: 350
  loop : -0.55 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J  66 
 TYR   0.009   0.001   TYR B 552 
 PHE   0.007   0.001   PHE A 420 
 TRP   0.010   0.001   TRP A 490 
 HIS   0.002   0.000   HIS J  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.11 ( 8014)
  covalent geometry    : angle       0.54347 /  0.31 (10912)
  SS BOND              : bond        0.00263 /  0.13 (    4)
  SS BOND              : angle       0.71551 /  0.37 (    8)
  hydrogen bonds       : bond        0.10609 /  6.67 (  251)
  hydrogen bonds       : angle       7.77971 /  5.78 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.268 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7789 (m-80) cc_final: 0.7230 (m-10)
REVERT: H  102 PHE cc_start: 0.6371 (m-80) cc_final: 0.6047 (t80)
REVERT: J   43 LYS cc_start: 0.7149 (mtmt) cc_final: 0.6559 (mttp)
REVERT: J   82 SER cc_start: 0.6827 (m) cc_final: 0.6546 (p)
REVERT: J  102 PHE cc_start: 0.6642 (m-80) cc_final: 0.6231 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 140
  average time/residue: 0.0665
  time to fit residues: 13.6841
Evaluate side-chains
  112 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
K  79 GLN
L  32 ASN
L  79 GLN
A 545 GLN
A 558 ASN
A 676 HIS
B 527 ASN
B 545 GLN
B 609 GLN
B 676 HIS
J  39 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.181697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.154163 restraints weight = 8498.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.68
r_work: 0.3626 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8018  Z= 0.134
  Angle     :  0.548   9.357  10920  Z= 0.284
  Chirality :  0.044   0.145   1172
  Planarity :  0.004   0.032   1394
  Dihedral  :  4.869  38.107   1075
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.10 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.26), residues: 976
  helix: -1.20 (1.53), residues: 12
  sheet:  0.02 (0.27), residues: 348
  loop : -0.57 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 627 
 TYR   0.016   0.001   TYR B 552 
 PHE   0.018   0.002   PHE B 630 
 TRP   0.014   0.002   TRP L  96 
 HIS   0.002   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 8014)
  covalent geometry    : angle       0.54684 /  0.28 (10912)
  SS BOND              : bond        0.00256 /  0.13 (    4)
  SS BOND              : angle       1.38751 /  0.71 (    8)
  hydrogen bonds       : bond        0.03194 /  2.14 (  251)
  hydrogen bonds       : angle       5.73956 /  4.20 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.279 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7859 (m-80) cc_final: 0.7287 (m-80)
REVERT: H  102 PHE cc_start: 0.6306 (m-80) cc_final: 0.6017 (t80)
REVERT: A  425 MET cc_start: 0.8757 (mtt) cc_final: 0.8349 (mtt)
REVERT: A  609 GLN cc_start: 0.7640 (mm110) cc_final: 0.7185 (mp10)
REVERT: B  425 MET cc_start: 0.8798 (mtt) cc_final: 0.8377 (mtt)
REVERT: B  631 ASP cc_start: 0.7083 (t70) cc_final: 0.6761 (m-30)
REVERT: J  102 PHE cc_start: 0.6513 (m-80) cc_final: 0.5996 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0520
  time to fit residues: 9.3522
Evaluate side-chains
  120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  469 ASN
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   51 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.1184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.178605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151456 restraints weight = 8383.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.65
r_work: 0.3594 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8018  Z= 0.151
  Angle     :  0.559  10.078  10920  Z= 0.289
  Chirality :  0.044   0.145   1172
  Planarity :  0.004   0.035   1394
  Dihedral  :  4.958  39.040   1074
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  :  8.93 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 976
  helix: -1.44 (1.49), residues: 12
  sheet: -0.11 (0.27), residues: 364
  loop : -0.70 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 627 
 TYR   0.015   0.001   TYR B 552 
 PHE   0.011   0.002   PHE B 420 
 TRP   0.015   0.002   TRP K  96 
 HIS   0.002   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 8014)
  covalent geometry    : angle       0.55784 /  0.29 (10912)
  SS BOND              : bond        0.00350 /  0.17 (    4)
  SS BOND              : angle       1.52913 /  0.87 (    8)
  hydrogen bonds       : bond        0.03192 /  2.16 (  251)
  hydrogen bonds       : angle       5.57933 /  4.06 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.208 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7932 (m-80) cc_final: 0.7276 (m-80)
REVERT: H  102 PHE cc_start: 0.6375 (m-80) cc_final: 0.5955 (t80)
REVERT: A  425 MET cc_start: 0.8777 (mtt) cc_final: 0.8453 (mtt)
REVERT: B  425 MET cc_start: 0.8864 (mtt) cc_final: 0.8546 (mtt)
REVERT: B  631 ASP cc_start: 0.7185 (t70) cc_final: 0.6862 (m-30)
REVERT: J  102 PHE cc_start: 0.6550 (m-80) cc_final: 0.6048 (t80)
  outliers start: 21
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0515
  time to fit residues: 10.1122
Evaluate side-chains
  128 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   51 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0470
   chunk 27 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.0086

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.179830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.153475 restraints weight = 8475.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.62
r_work: 0.3600 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8018  Z= 0.140
  Angle     :  0.553  10.425  10920  Z= 0.285
  Chirality :  0.044   0.142   1172
  Planarity :  0.004   0.032   1394
  Dihedral  :  4.990  39.870   1074
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  :  9.76 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.26), residues: 976
  helix: -1.42 (1.48), residues: 12
  sheet: -0.21 (0.27), residues: 364
  loop : -0.76 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 627 
 TYR   0.015   0.001   TYR B 552 
 PHE   0.010   0.002   PHE K  98 
 TRP   0.014   0.002   TRP L  96 
 HIS   0.002   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 8014)
  covalent geometry    : angle       0.55106 /  0.28 (10912)
  SS BOND              : bond        0.00201 /  0.10 (    4)
  SS BOND              : angle       1.84013 /  1.11 (    8)
  hydrogen bonds       : bond        0.03067 /  2.09 (  251)
  hydrogen bonds       : angle       5.39899 /  3.91 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.260 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7893 (m-80) cc_final: 0.7291 (m-80)
REVERT: H  102 PHE cc_start: 0.6437 (m-80) cc_final: 0.6232 (m-80)
REVERT: A  425 MET cc_start: 0.8770 (mtt) cc_final: 0.8436 (mtt)
REVERT: B  425 MET cc_start: 0.8850 (mtt) cc_final: 0.8533 (mtt)
REVERT: J  102 PHE cc_start: 0.6445 (m-80) cc_final: 0.5980 (t80)
  outliers start: 25
  outliers final: 21
  residues processed: 127
  average time/residue: 0.0525
  time to fit residues: 10.4362
Evaluate side-chains
  128 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0030
   chunk 52 optimal weight:    0.0070
   chunk 76 optimal weight:    0.0770
   chunk 47 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.6170

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.180444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.154411 restraints weight = 8388.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.57
r_work: 0.3633 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   8018  Z= 0.105
  Angle     :  0.524  10.590  10920  Z= 0.269
  Chirality :  0.042   0.137   1172
  Planarity :  0.003   0.030   1394
  Dihedral  :  4.821  39.385   1074
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.55 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.26), residues: 976
  helix: -1.33 (1.48), residues: 12
  sheet: -0.13 (0.27), residues: 362
  loop : -0.65 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 627 
 TYR   0.013   0.001   TYR J  58 
 PHE   0.007   0.001   PHE A 420 
 TRP   0.012   0.001   TRP A 490 
 HIS   0.002   0.000   HIS J  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.10 ( 8014)
  covalent geometry    : angle       0.52235 /  0.27 (10912)
  SS BOND              : bond        0.00314 /  0.16 (    4)
  SS BOND              : angle       1.39920 /  0.79 (    8)
  hydrogen bonds       : bond        0.02796 /  1.91 (  251)
  hydrogen bonds       : angle       5.18606 /  3.76 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.383 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7899 (m-80) cc_final: 0.7247 (m-80)
REVERT: H  102 PHE cc_start: 0.6395 (m-80) cc_final: 0.6190 (m-80)
REVERT: A  425 MET cc_start: 0.8751 (mtt) cc_final: 0.8383 (mtt)
REVERT: B  425 MET cc_start: 0.8777 (mtt) cc_final: 0.8364 (mtt)
REVERT: J  102 PHE cc_start: 0.6293 (m-80) cc_final: 0.5837 (t80)
  outliers start: 18
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0603
  time to fit residues: 11.9168
Evaluate side-chains
  122 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0370
   chunk 63 optimal weight:    0.0270
   chunk 70 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 94 optimal weight:    0.4980
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.3916

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.182650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.156900 restraints weight = 8355.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.53
r_work: 0.3661 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8018  Z= 0.089
  Angle     :  0.504  10.433  10920  Z= 0.258
  Chirality :  0.042   0.134   1172
  Planarity :  0.003   0.032   1394
  Dihedral  :  4.693  38.930   1074
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 11.07 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 976
  helix: -1.25 (1.49), residues: 12
  sheet: -0.06 (0.27), residues: 362
  loop : -0.59 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 627 
 TYR   0.013   0.001   TYR B 552 
 PHE   0.029   0.002   PHE A 630 
 TRP   0.011   0.001   TRP A 490 
 HIS   0.003   0.000   HIS J  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00195 /  0.09 ( 8014)
  covalent geometry    : angle       0.50378 /  0.26 (10912)
  SS BOND              : bond        0.00300 /  0.15 (    4)
  SS BOND              : angle       1.05256 /  0.57 (    8)
  hydrogen bonds       : bond        0.02677 /  1.81 (  251)
  hydrogen bonds       : angle       4.99432 /  3.62 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.228 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7879 (m-80) cc_final: 0.7236 (m-80)
REVERT: H  102 PHE cc_start: 0.6345 (m-80) cc_final: 0.5811 (t80)
REVERT: A  425 MET cc_start: 0.8686 (mtt) cc_final: 0.8280 (mtt)
REVERT: A  584 GLN cc_start: 0.6269 (pt0) cc_final: 0.5997 (pm20)
REVERT: B  425 MET cc_start: 0.8755 (mtt) cc_final: 0.8453 (mtt)
REVERT: J  102 PHE cc_start: 0.6259 (m-80) cc_final: 0.5787 (t80)
  outliers start: 23
  outliers final: 21
  residues processed: 122
  average time/residue: 0.0611
  time to fit residues: 11.6311
Evaluate side-chains
  124 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   32 PHE
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0070
   chunk 72 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 433 GLN
J  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.181245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.155416 restraints weight = 8396.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.54
r_work: 0.3648 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8018  Z= 0.106
  Angle     :  0.519  10.810  10920  Z= 0.265
  Chirality :  0.042   0.137   1172
  Planarity :  0.003   0.034   1394
  Dihedral  :  4.718  39.577   1074
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.02 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.26), residues: 976
  helix: -1.33 (1.46), residues: 12
  sheet: -0.10 (0.27), residues: 364
  loop : -0.64 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 627 
 TYR   0.012   0.001   TYR B 552 
 PHE   0.023   0.002   PHE B 630 
 TRP   0.010   0.001   TRP A 490 
 HIS   0.002   0.001   HIS J  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 8014)
  covalent geometry    : angle       0.51770 /  0.26 (10912)
  SS BOND              : bond        0.00265 /  0.13 (    4)
  SS BOND              : angle       1.25509 /  0.66 (    8)
  hydrogen bonds       : bond        0.02747 /  1.87 (  251)
  hydrogen bonds       : angle       5.00428 /  3.62 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: H  102 PHE cc_start: 0.6370 (m-80) cc_final: 0.5891 (t80)
REVERT: A  425 MET cc_start: 0.8697 (mtt) cc_final: 0.8305 (mtt)
REVERT: A  584 GLN cc_start: 0.6279 (pt0) cc_final: 0.5990 (pm20)
REVERT: B  425 MET cc_start: 0.8754 (mtt) cc_final: 0.8431 (mtt)
REVERT: J  102 PHE cc_start: 0.6320 (m-80) cc_final: 0.5841 (t80)
  outliers start: 24
  outliers final: 23
  residues processed: 124
  average time/residue: 0.0585
  time to fit residues: 11.4531
Evaluate side-chains
  128 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   63 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    2.3188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.143140 restraints weight = 8649.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.69
r_work: 0.3515 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   8018  Z= 0.280
  Angle     :  0.691  10.660  10920  Z= 0.359
  Chirality :  0.049   0.158   1172
  Planarity :  0.004   0.035   1394
  Dihedral  :  5.561  42.839   1074
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.43 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.26), residues: 976
  helix: -2.44 (1.24), residues: 12
  sheet: -0.55 (0.26), residues: 372
  loop : -0.89 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 424 
 TYR   0.018   0.002   TYR B 552 
 PHE   0.022   0.003   PHE B 630 
 TRP   0.020   0.003   TRP B 525 
 HIS   0.004   0.001   HIS L  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00661 /  0.28 ( 8014)
  covalent geometry    : angle       0.68844 /  0.36 (10912)
  SS BOND              : bond        0.00303 /  0.15 (    4)
  SS BOND              : angle       2.36634 /  1.22 (    8)
  hydrogen bonds       : bond        0.03880 /  2.65 (  251)
  hydrogen bonds       : angle       5.92874 /  4.22 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.349 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7937 (m-80) cc_final: 0.7234 (m-80)
REVERT: A  425 MET cc_start: 0.8849 (mtt) cc_final: 0.8640 (mtt)
REVERT: A  449 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6878 (m)
REVERT: A  584 GLN cc_start: 0.6689 (pt0) cc_final: 0.6193 (pm20)
REVERT: B  418 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6770 (m-30)
REVERT: B  425 MET cc_start: 0.8899 (mtt) cc_final: 0.8672 (mtt)
REVERT: J  102 PHE cc_start: 0.6705 (m-80) cc_final: 0.6175 (t80)
  outliers start: 29
  outliers final: 22
  residues processed: 123
  average time/residue: 0.0534
  time to fit residues: 10.7418
Evaluate side-chains
  123 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   63 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  469 ASN
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 87 optimal weight:    0.0570
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5298

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.180597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155897 restraints weight = 8377.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.38
r_work: 0.3650 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8018  Z= 0.104
  Angle     :  0.547  12.195  10920  Z= 0.281
  Chirality :  0.043   0.161   1172
  Planarity :  0.003   0.033   1394
  Dihedral  :  5.079  40.997   1074
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.98 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.26), residues: 976
  helix: -1.17 (1.54), residues: 12
  sheet: -0.21 (0.27), residues: 362
  loop : -0.74 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 627 
 TYR   0.014   0.001   TYR H  58 
 PHE   0.018   0.002   PHE B 630 
 TRP   0.013   0.001   TRP A 490 
 HIS   0.005   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 ( 8014)
  covalent geometry    : angle       0.54439 /  0.28 (10912)
  SS BOND              : bond        0.00519 /  0.26 (    4)
  SS BOND              : angle       2.20612 /  1.25 (    8)
  hydrogen bonds       : bond        0.02892 /  1.97 (  251)
  hydrogen bonds       : angle       5.40070 /  3.88 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.177 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7922 (m-80) cc_final: 0.7176 (m-80)
REVERT: A  425 MET cc_start: 0.8779 (mtt) cc_final: 0.8426 (mtt)
REVERT: A  584 GLN cc_start: 0.6482 (pt0) cc_final: 0.6089 (pm20)
REVERT: B  425 MET cc_start: 0.8798 (mtt) cc_final: 0.8470 (mtt)
REVERT: J  102 PHE cc_start: 0.6417 (m-80) cc_final: 0.5812 (t80)
  outliers start: 22
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0631
  time to fit residues: 11.7703
Evaluate side-chains
  123 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  469 ASN
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.179569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.154827 restraints weight = 8377.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.38
r_work: 0.3638 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8018  Z= 0.132
  Angle     :  0.567  11.131  10920  Z= 0.291
  Chirality :  0.043   0.142   1172
  Planarity :  0.004   0.032   1394
  Dihedral  :  4.937  41.672   1073
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.10 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.26), residues: 976
  helix: -1.01 (1.57), residues: 12
  sheet: -0.25 (0.27), residues: 366
  loop : -0.76 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 627 
 TYR   0.015   0.001   TYR H  58 
 PHE   0.020   0.002   PHE B 630 
 TRP   0.012   0.002   TRP K  96 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8014)
  covalent geometry    : angle       0.56347 /  0.29 (10912)
  SS BOND              : bond        0.00289 /  0.14 (    4)
  SS BOND              : angle       2.47114 /  1.39 (    8)
  hydrogen bonds       : bond        0.02982 /  2.03 (  251)
  hydrogen bonds       : angle       5.35520 /  3.84 (  840)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.283 
Fit side-chains
REVERT: H   59 TYR cc_start: 0.7954 (m-80) cc_final: 0.7695 (m-80)
REVERT: A  425 MET cc_start: 0.8753 (mtt) cc_final: 0.8539 (mtt)
REVERT: A  584 GLN cc_start: 0.6497 (pt0) cc_final: 0.5888 (pm20)
REVERT: B  425 MET cc_start: 0.8781 (mtt) cc_final: 0.8449 (mtt)
REVERT: J  102 PHE cc_start: 0.6432 (m-80) cc_final: 0.5796 (t80)
  outliers start: 21
  outliers final: 19
  residues processed: 116
  average time/residue: 0.0584
  time to fit residues: 10.7421
Evaluate side-chains
  120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain K residue   19 VAL
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain A residue  469 ASN
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  469 ASN
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  634 THR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   28 THR
Chi-restraints excluded: chain J residue   92 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.179212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.154696 restraints weight = 8381.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.36
r_work: 0.3636 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8018  Z= 0.138
  Angle     :  0.575  11.078  10920  Z= 0.294
  Chirality :  0.044   0.143   1172
  Planarity :  0.004   0.032   1394
  Dihedral  :  4.984  44.271   1073
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.45 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.26), residues: 976
  helix: -0.95 (1.59), residues: 12
  sheet: -0.28 (0.27), residues: 366
  loop : -0.78 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 627 
 TYR   0.014   0.001   TYR A 552 
 PHE   0.019   0.002   PHE H  29 
 TRP   0.012   0.002   TRP K  96 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 8014)
  covalent geometry    : angle       0.57209 /  0.29 (10912)
  SS BOND              : bond        0.00297 /  0.15 (    4)
  SS BOND              : angle       2.37365 /  1.33 (    8)
  hydrogen bonds       : bond        0.03013 /  2.05 (  251)
  hydrogen bonds       : angle       5.37203 /  3.86 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1763.46 seconds
wall clock time: 30 minutes 56.87 seconds (1856.87 seconds total)