Starting phenix.real_space_refine
on Sat Oct 11 10:48:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wh8_37533/10_2025/8wh8_37533.map"
  }
  resolution = 3.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     252      5.49       5
     S      29      5.16       5
     C    8263      2.51       5
     N    2636      2.21       5
     O    3124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14304
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 766
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "B"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 617
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 662
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    Chain: "D"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 695
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "F"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 710
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "G"
      Number of atoms: 700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 700
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2544
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2581
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "K"
      Number of atoms: 3592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3592
          Classifications: {'peptide': 443}
          Link IDs: {'PTRANS': 16, 'TRANS': 426}
          Chain breaks: 1
    Chain: "K"
      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: 3.50, per 1000 atoms: 0.24
  Number of scatterers: 14304
  At special positions: 0
  Unit cell: (131.76, 138.24, 117.72, 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      29     16.00
     P     252     15.00
     O    3124      8.00
     N    2636      7.00
     C    8263      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: 1.12
  Conformation dependent library (CDL) restraints added in 480.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      63.6% alpha, 4.4% beta
      99 base pairs and 194 stacking pairs defined.
    Time for finding SS restraints: 2.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.524A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.911A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.804A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.918A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.566A  pdb=" N   GLY B  28 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.055A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 46 through 75
      removed outlier: 4.081A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.625A  pdb=" N   ILE C  84 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 98
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 109
      removed outlier: 3.522A  pdb=" N   MET D  84 " --> pdb=" O   SER D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.604A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 149
      removed outlier: 3.822A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 55
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 87 through 114
      removed outlier: 3.680A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.711A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 40
    Processing helix  chain 'F' and resid 50 through 75
      removed outlier: 4.243A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.961A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 75
      removed outlier: 4.423A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG G  72 " --> pdb=" O   GLY G  68 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP G  73 " --> pdb=" O   ASN G  69 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.511A  pdb=" N   ILE G  84 " --> pdb=" O   VAL G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 98
    Processing helix  chain 'H' and resid 62 through 74
      removed outlier: 3.702A  pdb=" N   LYS H  68 " --> pdb=" O   ILE H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 109
      removed outlier: 3.553A  pdb=" N   MET H  87 " --> pdb=" O   ALA H  83 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   SER H  89 " --> pdb=" O   GLY H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 115 through 126
    Processing helix  chain 'H' and resid 129 through 148
      removed outlier: 3.926A  pdb=" N   LYS H 133 " --> pdb=" O   GLY H 129 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 204 through 220
    Processing helix  chain 'K' and resid 234 through 244
    Processing helix  chain 'K' and resid 258 through 272
      removed outlier: 3.919A  pdb=" N   LEU K 262 " --> pdb=" O   PRO K 258 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 286 through 294
      removed outlier: 3.957A  pdb=" N   GLU K 290 " --> pdb=" O   ASN K 286 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ARG K 292 " --> pdb=" O   ARG K 288 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 310 through 317
    Processing helix  chain 'K' and resid 317 through 323
      removed outlier: 4.068A  pdb=" N   ILE K 321 " --> pdb=" O   ASP K 317 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ARG K 323 " --> pdb=" O   LYS K 319 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 334 through 339
    Processing helix  chain 'K' and resid 343 through 352
      removed outlier: 3.874A  pdb=" N   HIS K 351 " --> pdb=" O   ARG K 347 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LEU K 352 " --> pdb=" O   GLU K 348 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 369 through 380
    Processing helix  chain 'K' and resid 416 through 425
      removed outlier: 3.651A  pdb=" N   ILE K 423 " --> pdb=" O   LYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 453 through 465
    Processing helix  chain 'K' and resid 488 through 499
    Processing helix  chain 'K' and resid 500 through 508
    Processing helix  chain 'K' and resid 518 through 522
    Processing helix  chain 'K' and resid 523 through 536
    Processing helix  chain 'K' and resid 550 through 564
      removed outlier: 3.564A  pdb=" N   LYS K 563 " --> pdb=" O   TYR K 559 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 575 through 587
    Processing helix  chain 'K' and resid 623 through 635
      removed outlier: 4.161A  pdb=" N   ASP K 627 " --> pdb=" O   ASN K 623 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   CYS K 634 " --> pdb=" O   ALA K 630 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 653 through 676
      removed outlier: 3.654A  pdb=" N   VAL K 672 " --> pdb=" O   LEU K 668 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN K 675 " --> pdb=" O   VAL K 671 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY K 676 " --> pdb=" O   VAL K 672 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.148A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.462A  pdb=" N   ARG B  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.400A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'F' and resid 97 through 98
      removed outlier: 3.696A  pdb=" N   TYR F  98 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.507A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'K' and resid 278 through 280
      removed outlier: 6.609A  pdb=" N   ILE K 279 " --> pdb=" O   ILE K 308 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   LEU K 254 " --> pdb=" O   VAL K 331 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 443 through 450
      removed outlier: 3.586A  pdb=" N   MET K 448 " --> pdb=" O   ARG K 647 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER K 649 " --> pdb=" O   MET K 448 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   CYS K 615 " --> pdb=" O   TYR K 646 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU K 648 " --> pdb=" O   CYS K 615 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU K 617 " --> pdb=" O   LEU K 648 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   THR K 650 " --> pdb=" O   LEU K 617 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU K 544 " --> pdb=" O   ILE K 616 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 567 through 570
      removed outlier: 6.350A  pdb=" N   CYS K 568 " --> pdb=" O   LEU K 597 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    500 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      256 hydrogen bonds
      508 hydrogen bond angles
      0 basepair planarities
      99 basepair parallelities
      194 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1702
        1.28 -     1.42: 4706
        1.42 -     1.55: 7948
        1.55 -     1.69: 671
        1.69 -     1.82: 48
  Bond restraints: 15075
  Sorted by residual:
  bond pdb=" C   SER K 653 "
       pdb=" O   SER K 653 "
    ideal  model  delta    sigma   weight residual
    1.235  1.316 -0.081 1.02e-02 9.61e+03 6.26e+01
  bond pdb=" C   ILE K 235 "
       pdb=" O   ILE K 235 "
    ideal  model  delta    sigma   weight residual
    1.236  1.142  0.094 1.19e-02 7.06e+03 6.23e+01
  bond pdb=" C   VAL H 136 "
       pdb=" O   VAL H 136 "
    ideal  model  delta    sigma   weight residual
    1.237  1.148  0.089 1.14e-02 7.69e+03 6.04e+01
  bond pdb=" N   ASN K 222 "
       pdb=" CA  ASN K 222 "
    ideal  model  delta    sigma   weight residual
    1.457  1.538 -0.081 1.29e-02 6.01e+03 3.92e+01
  bond pdb=" C4  ADP K 801 "
       pdb=" C5  ADP K 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.97e+01
  ... (remaining 15070 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 20300
        3.05 -     6.09: 1036
        6.09 -     9.14: 71
        9.14 -    12.18: 7
       12.18 -    15.23: 2
  Bond angle restraints: 21416
  Sorted by residual:
  angle pdb=" O3'  DC I 107 "
        pdb=" C3'  DC I 107 "
        pdb=" C2'  DC I 107 "
      ideal   model   delta    sigma   weight residual
     111.50  126.73  -15.23 1.50e+00 4.44e-01 1.03e+02
  angle pdb=" O3'  DT J  50 "
        pdb=" C3'  DT J  50 "
        pdb=" C2'  DT J  50 "
      ideal   model   delta    sigma   weight residual
     111.50  125.51  -14.01 1.50e+00 4.44e-01 8.73e+01
  angle pdb=" N   ARG F  17 "
        pdb=" CA  ARG F  17 "
        pdb=" C   ARG F  17 "
      ideal   model   delta    sigma   weight residual
     111.14  101.23    9.91 1.08e+00 8.57e-01 8.41e+01
  angle pdb=" N   LEU K 259 "
        pdb=" CA  LEU K 259 "
        pdb=" C   LEU K 259 "
      ideal   model   delta    sigma   weight residual
     111.14  119.57   -8.43 1.08e+00 8.57e-01 6.09e+01
  angle pdb=" N   LYS H 104 "
        pdb=" CA  LYS H 104 "
        pdb=" C   LYS H 104 "
      ideal   model   delta    sigma   weight residual
     111.28  103.01    8.27 1.09e+00 8.42e-01 5.75e+01
  ... (remaining 21411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.66: 7149
       33.66 -    67.32: 1220
       67.32 -   100.97: 32
      100.97 -   134.63: 4
      134.63 -   168.29: 5
  Dihedral angle restraints: 8410
    sinusoidal: 5091
      harmonic: 3319
  Sorted by residual:
  dihedral pdb=" O2A ADP K 801 "
           pdb=" O3A ADP K 801 "
           pdb=" PA  ADP K 801 "
           pdb=" PB  ADP K 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  164.37  135.63     1      2.00e+01 2.50e-03 4.12e+01
  dihedral pdb=" C4' ADP K 801 "
           pdb=" C5' ADP K 801 "
           pdb=" O5' ADP K 801 "
           pdb=" PA  ADP K 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   92.83   87.17     1      2.00e+01 2.50e-03 2.28e+01
  dihedral pdb=" CA  VAL B  81 "
           pdb=" C   VAL B  81 "
           pdb=" N   THR B  82 "
           pdb=" CA  THR B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.38  -22.62     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 8407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2317
       0.148 -    0.295: 108
       0.295 -    0.443: 1
       0.443 -    0.590: 0
       0.590 -    0.738: 2
  Chirality restraints: 2428
  Sorted by residual:
  chirality pdb=" C3'  DT J  50 "
            pdb=" C4'  DT J  50 "
            pdb=" O3'  DT J  50 "
            pdb=" C2'  DT J  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.92   -0.74 2.00e-01 2.50e+01 1.36e+01
  chirality pdb=" C3'  DC I 107 "
            pdb=" C4'  DC I 107 "
            pdb=" O3'  DC I 107 "
            pdb=" C2'  DC I 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.96   -0.70 2.00e-01 2.50e+01 1.24e+01
  chirality pdb=" CA  LEU K 372 "
            pdb=" N   LEU K 372 "
            pdb=" C   LEU K 372 "
            pdb=" CB  LEU K 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.74e+00
  ... (remaining 2425 not shown)

  Planarity restraints: 1833
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H 148 "    0.024 2.00e-02 2.50e+03   4.73e-02 2.23e+01
        pdb=" C   SER H 148 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   SER H 148 "    0.030 2.00e-02 2.50e+03
        pdb=" N   SER H 149 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU K 376 "    0.021 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" C   LEU K 376 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   LEU K 376 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN K 377 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN K 277 "   -0.020 2.00e-02 2.50e+03   4.14e-02 1.71e+01
        pdb=" C   ASN K 277 "    0.072 2.00e-02 2.50e+03
        pdb=" O   ASN K 277 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA K 278 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1830 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3714
        2.82 -     3.34: 13538
        3.34 -     3.86: 25280
        3.86 -     4.38: 30863
        4.38 -     4.90: 43590
  Nonbonded interactions: 116985
  Sorted by model distance:
  nonbonded pdb=" CG2 VAL K 516 "
            pdb=" CG1 ILE K 519 "
     model   vdw
     2.300 3.860
  nonbonded pdb=" CD1 ILE B  50 "
            pdb=" CG2 ILE E 119 "
     model   vdw
     2.307 3.880
  nonbonded pdb=" O   SER K 547 "
            pdb=" OG1 THR K 600 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OD1 ASN K 368 "
            pdb=" N   SER K 370 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   ASN K 466 "
            pdb=" OG1 THR K 467 "
     model   vdw
     2.325 3.040
  ... (remaining 116980 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 50 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 100)
  selection = (chain 'F' and resid 25 through 100)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 21 through 108)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.040
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
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   0.109  15075  Z= 0.821
  Angle     :  1.397  15.230  21416  Z= 0.972
  Chirality :  0.071   0.738   2428
  Planarity :  0.008   0.047   1833
  Dihedral  : 25.117 168.290   6268
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  7.44 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.86 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.21), residues: 1129
  helix: -1.60 (0.17), residues: 677
  sheet: -2.93 (0.58), residues: 62
  loop : -3.03 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 430 
 TYR   0.040   0.003   TYR K 329 
 PHE   0.028   0.003   PHE D  67 
 TRP   0.038   0.003   TRP K 217 
 HIS   0.016   0.002   HIS H  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.01275 (15075)
  covalent geometry    : angle       1.39726 (21416)
  hydrogen bonds       : bond        0.22102 (  756)
  hydrogen bonds       : angle       8.67054 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 326
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.6445 (m110) cc_final: 0.5761 (m-40)
REVERT: C   65 GLU cc_start: 0.7509 (tp30) cc_final: 0.7297 (tp30)
REVERT: C   75 LYS cc_start: 0.8499 (mttp) cc_final: 0.8234 (tmtt)
REVERT: E   54 TYR cc_start: 0.8331 (m-80) cc_final: 0.7823 (m-80)
REVERT: E  123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8733 (m-30)
REVERT: F   52 GLU cc_start: 0.7781 (tp30) cc_final: 0.7317 (tp30)
REVERT: G   36 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8702 (mtpt)
REVERT: H  113 THR cc_start: 0.9186 (m) cc_final: 0.8891 (p)
REVERT: H  141 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (mtmt)
REVERT: K  269 ILE cc_start: 0.8514 (tt) cc_final: 0.8306 (mt)
REVERT: K  296 MET cc_start: 0.8179 (mtp) cc_final: 0.7514 (mmp)
REVERT: K  432 MET cc_start: 0.6988 (mmm) cc_final: 0.6731 (tpt)
REVERT: K  446 ILE cc_start: 0.7555 (mt) cc_final: 0.7058 (tp)
REVERT: K  452 MET cc_start: 0.7877 (ttp) cc_final: 0.7651 (ttt)
REVERT: K  626 MET cc_start: 0.8521 (mmt) cc_final: 0.8311 (mmm)
REVERT: K  667 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6737 (mptt)
REVERT: K  669 GLU cc_start: 0.8623 (tp30) cc_final: 0.8340 (tp30)
  outliers start: 7
  outliers final: 1
  residues processed: 328
  average time/residue: 0.1820
  time to fit residues: 78.4722
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  211 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  93 GLN
D 120 GLN
K 206 GLN
K 286 ASN
K 366 GLN
K 462 HIS
** K 492 GLN ** 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 = 0.3746 r_free = 0.3746 target = 0.105210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.070093 restraints weight = 40184.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.070587 restraints weight = 22137.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.070847 restraints weight = 15451.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.071155 restraints weight = 14706.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.071336 restraints weight = 13621.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  15075  Z= 0.322
  Angle     :  0.788  10.085  21416  Z= 0.442
  Chirality :  0.045   0.187   2428
  Planarity :  0.006   0.045   1833
  Dihedral  : 29.302 175.309   3977
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.85 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.94 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.24), residues: 1129
  helix:  0.79 (0.19), residues: 685
  sheet: -2.64 (0.56), residues: 60
  loop : -2.54 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  30 
 TYR   0.019   0.002   TYR G  51 
 PHE   0.024   0.002   PHE E  67 
 TRP   0.018   0.003   TRP K 217 
 HIS   0.012   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00749 (15075)
  covalent geometry    : angle       0.78808 (21416)
  hydrogen bonds       : bond        0.07604 (  756)
  hydrogen bonds       : angle       4.17369 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.8549 (mttm) cc_final: 0.8237 (ttmm)
REVERT: A  123 ASP cc_start: 0.8885 (m-30) cc_final: 0.8680 (m-30)
REVERT: B   26 ILE cc_start: 0.9118 (pt) cc_final: 0.8868 (mt)
REVERT: B   93 GLN cc_start: 0.8385 (mt0) cc_final: 0.8131 (mt0)
REVERT: C   42 GLU cc_start: 0.8105 (tp30) cc_final: 0.7851 (mp0)
REVERT: C   65 GLU cc_start: 0.8263 (tp30) cc_final: 0.7860 (tp30)
REVERT: C   75 LYS cc_start: 0.8574 (mttp) cc_final: 0.8224 (tmtt)
REVERT: C   82 ARG cc_start: 0.8715 (tpt170) cc_final: 0.8404 (tpt170)
REVERT: D   67 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8589 (m-80)
REVERT: E   54 TYR cc_start: 0.8312 (m-80) cc_final: 0.7962 (m-80)
REVERT: H  138 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: K  296 MET cc_start: 0.8010 (mtp) cc_final: 0.7479 (mmp)
REVERT: K  452 MET cc_start: 0.7882 (ttp) cc_final: 0.7602 (ttt)
REVERT: K  486 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (mm)
REVERT: K  516 VAL cc_start: 0.8119 (t) cc_final: 0.7865 (t)
REVERT: K  570 ILE cc_start: 0.9106 (pt) cc_final: 0.8620 (mp)
REVERT: K  608 ASN cc_start: 0.7900 (t0) cc_final: 0.7292 (p0)
REVERT: K  626 MET cc_start: 0.8629 (mmt) cc_final: 0.8409 (mmm)
  outliers start: 34
  outliers final: 19
  residues processed: 203
  average time/residue: 0.1438
  time to fit residues: 41.2117
Evaluate side-chains
  167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  147 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  486 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  631 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 102 optimal weight:   30.0000
   chunk 98 optimal weight:    0.0050
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 132 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 130 optimal weight:   20.0000
   chunk 64 optimal weight:    0.0370
   overall best weight:    1.1876

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
E  55 GLN
E  85 GLN
G  85 GLN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.108031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.072866 restraints weight = 40075.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.074103 restraints weight = 21551.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.074654 restraints weight = 14088.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.074927 restraints weight = 13481.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.074933 restraints weight = 12190.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.4547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15075  Z= 0.170
  Angle     :  0.602   8.230  21416  Z= 0.344
  Chirality :  0.037   0.150   2428
  Planarity :  0.004   0.035   1833
  Dihedral  : 28.777 179.232   3973
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.79 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.26), residues: 1129
  helix:  1.91 (0.20), residues: 691
  sheet: -2.19 (0.62), residues: 48
  loop : -2.09 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 134 
 TYR   0.011   0.001   TYR G  51 
 PHE   0.015   0.001   PHE H  67 
 TRP   0.019   0.002   TRP K 217 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (15075)
  covalent geometry    : angle       0.60171 (21416)
  hydrogen bonds       : bond        0.05441 (  756)
  hydrogen bonds       : angle       3.48924 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: C   42 GLU cc_start: 0.8027 (tp30) cc_final: 0.7793 (mp0)
REVERT: C   65 GLU cc_start: 0.8413 (tp30) cc_final: 0.7808 (tp30)
REVERT: C   75 LYS cc_start: 0.8638 (mttp) cc_final: 0.8310 (tmtt)
REVERT: C   82 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8389 (tpt170)
REVERT: C   85 GLN cc_start: 0.8872 (tp40) cc_final: 0.8644 (tp40)
REVERT: C   91 ASP cc_start: 0.7685 (t0) cc_final: 0.7270 (t0)
REVERT: D   67 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (m-80)
REVERT: E   54 TYR cc_start: 0.8200 (m-80) cc_final: 0.7874 (m-80)
REVERT: E   56 LYS cc_start: 0.6595 (pttt) cc_final: 0.5602 (tppt)
REVERT: E   73 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6879 (mt-10)
REVERT: G   57 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: G   74 ASN cc_start: 0.8865 (m-40) cc_final: 0.7878 (t0)
REVERT: K  212 TRP cc_start: 0.7912 (t-100) cc_final: 0.7517 (t-100)
REVERT: K  296 MET cc_start: 0.8305 (mtp) cc_final: 0.7433 (mmp)
REVERT: K  575 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7809 (pptt)
REVERT: K  608 ASN cc_start: 0.8054 (t0) cc_final: 0.7314 (p0)
REVERT: K  626 MET cc_start: 0.8613 (mmt) cc_final: 0.8383 (mmm)
  outliers start: 24
  outliers final: 15
  residues processed: 192
  average time/residue: 0.1343
  time to fit residues: 37.3017
Evaluate side-chains
  166 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue  109 ASN
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  529 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 112 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 122 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 625 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.106071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.070541 restraints weight = 39977.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.071424 restraints weight = 21576.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.072238 restraints weight = 14582.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.072408 restraints weight = 13213.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.072451 restraints weight = 12473.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.5037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.199
  Angle     :  0.611   6.729  21416  Z= 0.349
  Chirality :  0.037   0.145   2428
  Planarity :  0.004   0.038   1833
  Dihedral  : 28.769 173.929   3973
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.99 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.26), residues: 1129
  helix:  2.11 (0.20), residues: 693
  sheet: -2.25 (0.59), residues: 60
  loop : -2.09 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 636 
 TYR   0.010   0.001   TYR D  65 
 PHE   0.014   0.001   PHE H  67 
 TRP   0.015   0.002   TRP K 217 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (15075)
  covalent geometry    : angle       0.61139 (21416)
  hydrogen bonds       : bond        0.05835 (  756)
  hydrogen bonds       : angle       3.50342 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.8017 (tp30) cc_final: 0.7801 (mp0)
REVERT: C   65 GLU cc_start: 0.8468 (tp30) cc_final: 0.7715 (tp30)
REVERT: C   75 LYS cc_start: 0.8726 (mttp) cc_final: 0.8351 (tptp)
REVERT: C   82 ARG cc_start: 0.8742 (tpt170) cc_final: 0.8387 (tpt170)
REVERT: D   67 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8524 (m-80)
REVERT: E   54 TYR cc_start: 0.8221 (m-80) cc_final: 0.7822 (m-80)
REVERT: E  108 ASN cc_start: 0.9450 (t0) cc_final: 0.9121 (t0)
REVERT: G   57 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: G   74 ASN cc_start: 0.8891 (m-40) cc_final: 0.7944 (t0)
REVERT: G   85 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8150 (tp-100)
REVERT: H  138 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: K  212 TRP cc_start: 0.7733 (t-100) cc_final: 0.7482 (t-100)
REVERT: K  296 MET cc_start: 0.8193 (mtp) cc_final: 0.7569 (mmp)
REVERT: K  486 LEU cc_start: 0.8780 (mm) cc_final: 0.8559 (mm)
REVERT: K  608 ASN cc_start: 0.8129 (t0) cc_final: 0.7430 (p0)
REVERT: K  622 TRP cc_start: 0.8545 (OUTLIER) cc_final: 0.8248 (m-10)
REVERT: K  626 MET cc_start: 0.8666 (mmt) cc_final: 0.8120 (mmm)
  outliers start: 26
  outliers final: 18
  residues processed: 176
  average time/residue: 0.1252
  time to fit residues: 32.3592
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 108 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 125 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 133 optimal weight:    8.9990
   chunk 118 optimal weight:    0.6980
   chunk 14 optimal weight:    0.1980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.108453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.073551 restraints weight = 39900.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.074880 restraints weight = 21511.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.075494 restraints weight = 13884.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.075773 restraints weight = 13045.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.075801 restraints weight = 11888.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.5360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15075  Z= 0.145
  Angle     :  0.562   6.859  21416  Z= 0.321
  Chirality :  0.035   0.253   2428
  Planarity :  0.003   0.037   1833
  Dihedral  : 28.435 171.797   3973
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.81 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.20 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.26), residues: 1129
  helix:  2.44 (0.21), residues: 693
  sheet: -1.89 (0.57), residues: 68
  loop : -1.89 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 431 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.009   0.001   PHE K 240 
 TRP   0.018   0.001   TRP K 217 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15075)
  covalent geometry    : angle       0.56197 (21416)
  hydrogen bonds       : bond        0.04736 (  756)
  hydrogen bonds       : angle       3.16673 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7949 (mt-10)
REVERT: C   65 GLU cc_start: 0.8503 (tp30) cc_final: 0.7799 (tp30)
REVERT: C   75 LYS cc_start: 0.8674 (mttp) cc_final: 0.8352 (tptp)
REVERT: C   82 ARG cc_start: 0.8692 (tpt170) cc_final: 0.8451 (tpt170)
REVERT: C   91 ASP cc_start: 0.7985 (t0) cc_final: 0.7712 (t70)
REVERT: D   67 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (m-80)
REVERT: D  118 GLU cc_start: 0.8610 (mp0) cc_final: 0.8219 (mp0)
REVERT: E   54 TYR cc_start: 0.8226 (m-80) cc_final: 0.7806 (m-80)
REVERT: E   56 LYS cc_start: 0.6795 (pttt) cc_final: 0.5847 (tppt)
REVERT: E  108 ASN cc_start: 0.9411 (t0) cc_final: 0.9041 (t0)
REVERT: G   57 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8393 (tm-30)
REVERT: G   73 ASP cc_start: 0.8618 (m-30) cc_final: 0.7891 (t0)
REVERT: G   74 ASN cc_start: 0.8800 (m-40) cc_final: 0.7947 (t0)
REVERT: G   85 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8064 (tp-100)
REVERT: K  212 TRP cc_start: 0.7862 (t-100) cc_final: 0.7585 (t-100)
REVERT: K  296 MET cc_start: 0.8252 (mtp) cc_final: 0.7666 (mmp)
REVERT: K  354 MET cc_start: 0.7798 (mtm) cc_final: 0.7289 (mtm)
REVERT: K  608 ASN cc_start: 0.8236 (t0) cc_final: 0.7515 (p0)
REVERT: K  622 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.8107 (m-10)
  outliers start: 23
  outliers final: 13
  residues processed: 176
  average time/residue: 0.1258
  time to fit residues: 32.5451
Evaluate side-chains
  158 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:   20.0000
   chunk 90 optimal weight:    0.9990
   chunk 120 optimal weight:    6.9990
   chunk 113 optimal weight:    0.3980
   chunk 89 optimal weight:   10.0000
   chunk 112 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 124 optimal weight:    8.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  93 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.108581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072650 restraints weight = 39960.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.074883 restraints weight = 21098.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.075283 restraints weight = 13049.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.075414 restraints weight = 11796.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.075479 restraints weight = 12342.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15075  Z= 0.144
  Angle     :  0.554   6.713  21416  Z= 0.315
  Chirality :  0.035   0.189   2428
  Planarity :  0.003   0.034   1833
  Dihedral  : 28.388 170.168   3973
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.16 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.09 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.26), residues: 1129
  helix:  2.51 (0.20), residues: 694
  sheet: -1.59 (0.60), residues: 68
  loop : -1.75 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 431 
 TYR   0.009   0.001   TYR D  65 
 PHE   0.009   0.001   PHE K 240 
 TRP   0.012   0.001   TRP K 265 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (15075)
  covalent geometry    : angle       0.55425 (21416)
  hydrogen bonds       : bond        0.04644 (  756)
  hydrogen bonds       : angle       3.09458 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7945 (mt-10)
REVERT: C   65 GLU cc_start: 0.8493 (tp30) cc_final: 0.7771 (tp30)
REVERT: C   75 LYS cc_start: 0.8661 (mttp) cc_final: 0.8367 (tptp)
REVERT: C   82 ARG cc_start: 0.8695 (tpt170) cc_final: 0.8461 (tpt170)
REVERT: C   91 ASP cc_start: 0.8003 (t0) cc_final: 0.7697 (t70)
REVERT: D   67 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8404 (m-80)
REVERT: D  118 GLU cc_start: 0.8566 (mp0) cc_final: 0.8202 (mp0)
REVERT: E   54 TYR cc_start: 0.8250 (m-80) cc_final: 0.7771 (m-80)
REVERT: E   56 LYS cc_start: 0.6806 (pttt) cc_final: 0.5872 (tppt)
REVERT: E  108 ASN cc_start: 0.9453 (t0) cc_final: 0.9076 (t0)
REVERT: E  118 THR cc_start: 0.9352 (m) cc_final: 0.8965 (p)
REVERT: G   57 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8341 (tm-30)
REVERT: G   73 ASP cc_start: 0.8503 (m-30) cc_final: 0.7817 (t0)
REVERT: G   74 ASN cc_start: 0.8732 (m-40) cc_final: 0.7941 (t0)
REVERT: G   78 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8271 (mtp-110)
REVERT: G   85 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8097 (tp-100)
REVERT: H   60 GLU cc_start: 0.8052 (tp30) cc_final: 0.7842 (tp30)
REVERT: K  212 TRP cc_start: 0.7891 (t-100) cc_final: 0.7605 (t-100)
REVERT: K  294 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6528 (pptt)
REVERT: K  296 MET cc_start: 0.8265 (mtp) cc_final: 0.7524 (mmp)
REVERT: K  608 ASN cc_start: 0.8321 (t0) cc_final: 0.7598 (p0)
REVERT: K  622 TRP cc_start: 0.8489 (OUTLIER) cc_final: 0.8256 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1254
  time to fit residues: 31.6535
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  294 LYS
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  478 ARG
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 104 optimal weight:    7.9990
   chunk 131 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.106501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.071359 restraints weight = 39544.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.072080 restraints weight = 22240.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072952 restraints weight = 15170.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.073024 restraints weight = 13943.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.073095 restraints weight = 12897.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  15075  Z= 0.191
  Angle     :  0.590   7.346  21416  Z= 0.334
  Chirality :  0.037   0.218   2428
  Planarity :  0.004   0.035   1833
  Dihedral  : 28.452 168.489   3973
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.25 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.58 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1129
  helix:  2.48 (0.20), residues: 692
  sheet: -1.59 (0.61), residues: 68
  loop : -1.90 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 134 
 TYR   0.010   0.001   TYR D  65 
 PHE   0.012   0.001   PHE K 240 
 TRP   0.014   0.001   TRP K 265 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (15075)
  covalent geometry    : angle       0.59010 (21416)
  hydrogen bonds       : bond        0.05390 (  756)
  hydrogen bonds       : angle       3.24157 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 142
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 GLU cc_start: 0.8547 (tp30) cc_final: 0.7898 (tp30)
REVERT: C   75 LYS cc_start: 0.8632 (mttp) cc_final: 0.8369 (tptp)
REVERT: C   82 ARG cc_start: 0.8677 (tpt170) cc_final: 0.8430 (tpt170)
REVERT: C   91 ASP cc_start: 0.8075 (t0) cc_final: 0.7756 (t70)
REVERT: D   67 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8451 (m-80)
REVERT: D  118 GLU cc_start: 0.8688 (mp0) cc_final: 0.8268 (mp0)
REVERT: E   54 TYR cc_start: 0.8205 (m-80) cc_final: 0.7692 (m-80)
REVERT: E   56 LYS cc_start: 0.6919 (pttt) cc_final: 0.5975 (tppt)
REVERT: E   73 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6155 (mt-10)
REVERT: G   57 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: G   73 ASP cc_start: 0.8643 (m-30) cc_final: 0.7931 (t0)
REVERT: G   74 ASN cc_start: 0.8876 (m-40) cc_final: 0.7981 (t0)
REVERT: G   78 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8261 (mtp-110)
REVERT: G   85 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8263 (tp-100)
REVERT: K  212 TRP cc_start: 0.7804 (t-100) cc_final: 0.7515 (t-100)
REVERT: K  265 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.6684 (m-10)
REVERT: K  294 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6602 (pptt)
REVERT: K  296 MET cc_start: 0.8252 (mtp) cc_final: 0.7668 (mmp)
REVERT: K  354 MET cc_start: 0.7587 (mtm) cc_final: 0.7090 (mtm)
REVERT: K  452 MET cc_start: 0.7599 (ttp) cc_final: 0.7102 (ttt)
REVERT: K  608 ASN cc_start: 0.8241 (t0) cc_final: 0.7612 (p0)
REVERT: K  622 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.8278 (m-10)
  outliers start: 34
  outliers final: 21
  residues processed: 171
  average time/residue: 0.1356
  time to fit residues: 33.3295
Evaluate side-chains
  163 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  265 TRP
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  294 LYS
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  478 ARG
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0000
   chunk 88 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 1 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0050
   overall best weight:    0.4800

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D 134 HIS
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 456 GLN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.109550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.075464 restraints weight = 39759.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.076167 restraints weight = 21923.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.076786 restraints weight = 15357.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077102 restraints weight = 13014.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.077186 restraints weight = 12323.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.6016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15075  Z= 0.136
  Angle     :  0.557  11.490  21416  Z= 0.313
  Chirality :  0.034   0.186   2428
  Planarity :  0.003   0.040   1833
  Dihedral  : 28.224 168.464   3973
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.81 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.32 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.26), residues: 1129
  helix:  2.63 (0.20), residues: 699
  sheet: -1.28 (0.63), residues: 68
  loop : -1.79 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  83 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.023   0.001   PHE K 240 
 TRP   0.014   0.001   TRP K 217 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (15075)
  covalent geometry    : angle       0.55706 (21416)
  hydrogen bonds       : bond        0.04316 (  756)
  hydrogen bonds       : angle       2.97111 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7954 (mt-10)
REVERT: C   65 GLU cc_start: 0.8569 (tp30) cc_final: 0.7990 (tp30)
REVERT: C   82 ARG cc_start: 0.8616 (tpt170) cc_final: 0.8337 (tpt170)
REVERT: C   91 ASP cc_start: 0.7819 (t0) cc_final: 0.7452 (t0)
REVERT: D   67 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8367 (m-80)
REVERT: D  118 GLU cc_start: 0.8519 (mp0) cc_final: 0.8188 (mp0)
REVERT: E   54 TYR cc_start: 0.8156 (m-80) cc_final: 0.7636 (m-80)
REVERT: E   56 LYS cc_start: 0.6941 (pttt) cc_final: 0.6129 (tptt)
REVERT: E  108 ASN cc_start: 0.9372 (t0) cc_final: 0.9162 (t0)
REVERT: E  118 THR cc_start: 0.9359 (m) cc_final: 0.8968 (p)
REVERT: E  120 MET cc_start: 0.8425 (mtm) cc_final: 0.8131 (mtm)
REVERT: G   57 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: G   73 ASP cc_start: 0.8457 (m-30) cc_final: 0.7824 (t0)
REVERT: G   74 ASN cc_start: 0.8678 (m-40) cc_final: 0.7925 (t0)
REVERT: G   78 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8113 (mtp-110)
REVERT: G   85 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8096 (tp-100)
REVERT: G   90 ASN cc_start: 0.8657 (t0) cc_final: 0.8191 (m-40)
REVERT: H   84 MET cc_start: 0.8419 (ttm) cc_final: 0.8035 (tpp)
REVERT: K  212 TRP cc_start: 0.7692 (t-100) cc_final: 0.7380 (t-100)
REVERT: K  294 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7063 (pttp)
REVERT: K  296 MET cc_start: 0.8199 (mtp) cc_final: 0.7708 (mmp)
REVERT: K  354 MET cc_start: 0.7539 (mtm) cc_final: 0.7104 (mtm)
REVERT: K  452 MET cc_start: 0.7485 (ttp) cc_final: 0.7196 (ttt)
REVERT: K  483 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7215 (pttm)
REVERT: K  488 ASN cc_start: 0.8710 (p0) cc_final: 0.8414 (p0)
REVERT: K  608 ASN cc_start: 0.8293 (t0) cc_final: 0.7707 (p0)
  outliers start: 21
  outliers final: 11
  residues processed: 177
  average time/residue: 0.1333
  time to fit residues: 34.1820
Evaluate side-chains
  166 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  213 LEU
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  294 LYS
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 95 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 120 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 130 optimal weight:    9.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
F  75 HIS
H  88 ASN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.105071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.069870 restraints weight = 39829.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070536 restraints weight = 22242.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.071353 restraints weight = 15327.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.071436 restraints weight = 14045.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.071545 restraints weight = 13001.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.6017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  15075  Z= 0.232
  Angle     :  0.633   8.370  21416  Z= 0.352
  Chirality :  0.039   0.350   2428
  Planarity :  0.004   0.043   1833
  Dihedral  : 28.480 164.551   3973
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.69 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.94 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1129
  helix:  2.45 (0.20), residues: 685
  sheet: -1.08 (0.66), residues: 55
  loop : -1.87 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  30 
 TYR   0.012   0.001   TYR B  72 
 PHE   0.030   0.001   PHE K 240 
 TRP   0.017   0.002   TRP K 265 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (15075)
  covalent geometry    : angle       0.63280 (21416)
  hydrogen bonds       : bond        0.05991 (  756)
  hydrogen bonds       : angle       3.37013 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6425 (p0)
REVERT: C   65 GLU cc_start: 0.8623 (tp30) cc_final: 0.7947 (tp30)
REVERT: C   82 ARG cc_start: 0.8676 (tpt170) cc_final: 0.8344 (tpt170)
REVERT: C   91 ASP cc_start: 0.8104 (t0) cc_final: 0.7708 (t0)
REVERT: D   67 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8429 (m-80)
REVERT: D  118 GLU cc_start: 0.8706 (mp0) cc_final: 0.8294 (mp0)
REVERT: E   54 TYR cc_start: 0.8107 (m-80) cc_final: 0.7485 (m-80)
REVERT: E   56 LYS cc_start: 0.7049 (pttt) cc_final: 0.6228 (tptt)
REVERT: E   73 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6472 (mt-10)
REVERT: G   57 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8457 (tm-30)
REVERT: G   73 ASP cc_start: 0.8672 (m-30) cc_final: 0.7965 (t0)
REVERT: G   74 ASN cc_start: 0.8935 (m-40) cc_final: 0.7986 (t0)
REVERT: G   78 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8160 (mtp-110)
REVERT: G   85 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8248 (tp-100)
REVERT: G   90 ASN cc_start: 0.8782 (t0) cc_final: 0.8316 (m-40)
REVERT: H   84 MET cc_start: 0.8771 (ttm) cc_final: 0.8493 (tpp)
REVERT: K  212 TRP cc_start: 0.7748 (t-100) cc_final: 0.7458 (t-100)
REVERT: K  265 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6987 (m-10)
REVERT: K  294 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6708 (pptt)
REVERT: K  296 MET cc_start: 0.8214 (mtp) cc_final: 0.7726 (mmp)
REVERT: K  452 MET cc_start: 0.7602 (ttp) cc_final: 0.7139 (ttt)
REVERT: K  608 ASN cc_start: 0.8373 (t0) cc_final: 0.7821 (p0)
  outliers start: 22
  outliers final: 15
  residues processed: 162
  average time/residue: 0.1347
  time to fit residues: 31.4996
Evaluate side-chains
  159 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  265 TRP
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  294 LYS
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  478 ARG
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 106 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** K 492 GLN ** 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 = 0.3798 r_free = 0.3798 target = 0.107774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073633 restraints weight = 39661.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.074122 restraints weight = 21782.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.074385 restraints weight = 16996.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.074517 restraints weight = 15407.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.074613 restraints weight = 14627.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.6230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15075  Z= 0.145
  Angle     :  0.585  11.303  21416  Z= 0.325
  Chirality :  0.036   0.293   2428
  Planarity :  0.004   0.040   1833
  Dihedral  : 28.230 165.473   3973
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.65 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.26), residues: 1129
  helix:  2.65 (0.20), residues: 692
  sheet: -1.00 (0.67), residues: 56
  loop : -1.77 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  30 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.034   0.001   PHE K 240 
 TRP   0.013   0.001   TRP K 265 
 HIS   0.001   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (15075)
  covalent geometry    : angle       0.58541 (21416)
  hydrogen bonds       : bond        0.04582 (  756)
  hydrogen bonds       : angle       3.06276 ( 1990)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7960 (mt-10)
REVERT: C   65 GLU cc_start: 0.8525 (tp30) cc_final: 0.7995 (tp30)
REVERT: C   82 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8256 (tpt170)
REVERT: C   91 ASP cc_start: 0.7892 (t0) cc_final: 0.7510 (t0)
REVERT: D   67 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8331 (m-80)
REVERT: D  118 GLU cc_start: 0.8548 (mp0) cc_final: 0.8185 (mp0)
REVERT: E   54 TYR cc_start: 0.8004 (m-80) cc_final: 0.7374 (m-80)
REVERT: E   56 LYS cc_start: 0.6991 (pttt) cc_final: 0.6194 (tptt)
REVERT: E   73 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6411 (mt-10)
REVERT: E  108 ASN cc_start: 0.9451 (t0) cc_final: 0.8928 (t0)
REVERT: E  118 THR cc_start: 0.9349 (m) cc_final: 0.8979 (p)
REVERT: G   57 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: G   73 ASP cc_start: 0.8510 (m-30) cc_final: 0.7826 (t0)
REVERT: G   74 ASN cc_start: 0.8820 (m-40) cc_final: 0.7962 (t0)
REVERT: G   78 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8106 (mtp-110)
REVERT: G   85 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8328 (tp-100)
REVERT: H   84 MET cc_start: 0.8456 (ttm) cc_final: 0.8167 (tpp)
REVERT: K  212 TRP cc_start: 0.7692 (t-100) cc_final: 0.7357 (t-100)
REVERT: K  294 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7143 (pttp)
REVERT: K  296 MET cc_start: 0.8211 (mtp) cc_final: 0.7882 (mmp)
REVERT: K  452 MET cc_start: 0.7549 (ttp) cc_final: 0.7266 (ttt)
REVERT: K  608 ASN cc_start: 0.8290 (t0) cc_final: 0.7777 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 164
  average time/residue: 0.1365
  time to fit residues: 32.2783
Evaluate side-chains
  158 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  294 LYS
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  478 ARG
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 96 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.106661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071039 restraints weight = 39538.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.072919 restraints weight = 19872.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.073253 restraints weight = 12987.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.073513 restraints weight = 11838.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.073607 restraints weight = 11507.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.6273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.169
  Angle     :  0.605  12.485  21416  Z= 0.336
  Chirality :  0.036   0.230   2428
  Planarity :  0.004   0.041   1833
  Dihedral  : 28.291 163.392   3973
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.83 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.26), residues: 1129
  helix:  2.63 (0.20), residues: 691
  sheet: -0.99 (0.67), residues: 56
  loop : -1.76 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  30 
 TYR   0.009   0.001   TYR K 325 
 PHE   0.036   0.001   PHE K 240 
 TRP   0.006   0.001   TRP K 217 
 HIS   0.002   0.000   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (15075)
  covalent geometry    : angle       0.60531 (21416)
  hydrogen bonds       : bond        0.05014 (  756)
  hydrogen bonds       : angle       3.16577 ( 1990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2456.65 seconds
wall clock time: 43 minutes 7.27 seconds (2587.27 seconds total)