Starting phenix.real_space_refine
on Thu Aug  6 06:35:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wh8_37533/08_2026/8wh8_37533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wh8_37533/08_2026/8wh8_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_37533/08_2026/8wh8_37533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wh8_37533/08_2026/8wh8_37533.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wh8_37533/08_2026/8wh8_37533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wh8_37533/08_2026/8wh8_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-2.2rc3-6140/lib/python3.11/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: 2.55, per 1000 atoms: 0.18
  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: 0.92
  Conformation dependent library (CDL) restraints added in 290.3 milliseconds
  

  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: 1.53
  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: 2.48

  Time building geometry restraints manager: 1.22 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=" C1'  DC I 125 "
       pdb=" N1   DC I 125 "
    ideal  model  delta    sigma   weight residual
    1.468  1.550 -0.082 1.40e-02 5.10e+03 3.40e+01
  ... (remaining 15070 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 20643
        3.47 -     6.93: 721
        6.93 -    10.40: 48
       10.40 -    13.86: 2
       13.86 -    17.33: 2
  Bond angle restraints: 21416
  Sorted by residual:
  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
  angle pdb=" O3'  DC I 107 "
        pdb=" C3'  DC I 107 "
        pdb=" C2'  DC I 107 "
      ideal   model   delta    sigma   weight residual
     109.40  126.73  -17.33 2.50e+00 1.60e-01 4.81e+01
  angle pdb=" N   GLU K 517 "
        pdb=" CA  GLU K 517 "
        pdb=" C   GLU K 517 "
      ideal   model   delta    sigma   weight residual
     113.38  105.39    7.99 1.17e+00 7.31e-01 4.66e+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 -    0.162: 2338
       0.162 -    0.323: 87
       0.323 -    0.485: 1
       0.485 -    0.646: 0
       0.646 -    0.808: 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     -2.73   -1.92   -0.81 2.00e-01 2.50e+01 1.63e+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     -2.73   -1.96   -0.77 2.00e-01 2.50e+01 1.50e+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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     12.400
  Find NCS groups from input model:        0.080
  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:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
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= 0.971
  Angle     :  1.424  17.330  21416  Z= 1.057
  Chirality :  0.076   0.808   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 are 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/Z
  covalent geometry    : bond        0.01299 /  0.97 (15075)
  covalent geometry    : angle       1.42441 /  1.06 (21416)
  hydrogen bonds       : bond        0.22102 / 14.89 (  756)
  hydrogen bonds       : angle       8.67054 /  5.95 ( 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  : 0.253 
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: 0.5760 (m-40)
REVERT: C   65 GLU cc_start: 0.7509 (tp30) cc_final: 0.7296 (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: 0.7824 (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: H  141 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8209 (mtmt)
REVERT: K  269 ILE cc_start: 0.8514 (tt) cc_final: 0.8305 (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: 0.6730 (tpt)
REVERT: K  446 ILE cc_start: 0.7555 (mt) cc_final: 0.7059 (tp)
REVERT: K  452 MET cc_start: 0.7877 (ttp) cc_final: 0.7650 (ttt)
REVERT: K  626 MET cc_start: 0.8521 (mmt) cc_final: 0.8312 (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: 0.8339 (tp30)
  outliers start: 7
  outliers final: 1
  residues processed: 328
  average time/residue: 0.1365
  time to fit residues: 60.0037
Evaluate side-chains
  167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   40.0000
   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...
A  68 GLN
D 120 GLN
E  85 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 = 0.3778 r_free = 0.3778 target = 0.107401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.070563 restraints weight = 39973.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.072642 restraints weight = 20180.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073979 restraints weight = 13700.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.074681 restraints weight = 11156.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.075007 restraints weight = 10090.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  15075  Z= 0.299
  Angle     :  0.886   9.666  21416  Z= 0.489
  Chirality :  0.056   0.363   2428
  Planarity :  0.006   0.057   1833
  Dihedral  : 29.509 174.623   3977
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.78 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.15 %
    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 are not related in a simple way.
  whole: -1.11 (0.24), residues: 1129
  helix:  0.45 (0.19), residues: 687
  sheet: -2.97 (0.58), residues: 70
  loop : -2.50 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 636 
 TYR   0.015   0.002   TYR K 325 
 PHE   0.021   0.003   PHE E  67 
 TRP   0.017   0.003   TRP K 217 
 HIS   0.008   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00637 /  0.30 (15075)
  covalent geometry    : angle       0.88630 /  0.49 (21416)
  hydrogen bonds       : bond        0.08479 /  5.75 (  756)
  hydrogen bonds       : angle       4.47020 /  3.15 ( 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
  208 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8536 (mt0) cc_final: 0.8197 (mt0)
REVERT: C   42 GLU cc_start: 0.8201 (tp30) cc_final: 0.7897 (mp0)
REVERT: C   65 GLU cc_start: 0.7866 (tp30) cc_final: 0.7636 (tp30)
REVERT: C   75 LYS cc_start: 0.8593 (mttp) cc_final: 0.8227 (tmtt)
REVERT: D   67 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8462 (m-80)
REVERT: E   54 TYR cc_start: 0.8322 (m-80) cc_final: 0.7835 (m-80)
REVERT: H   84 MET cc_start: 0.8580 (mtm) cc_final: 0.8362 (mtm)
REVERT: K  296 MET cc_start: 0.8050 (mtp) cc_final: 0.7400 (mmp)
REVERT: K  486 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8493 (mm)
REVERT: K  570 ILE cc_start: 0.9112 (pt) cc_final: 0.8629 (mp)
REVERT: K  608 ASN cc_start: 0.7916 (t0) cc_final: 0.7394 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 198
  average time/residue: 0.1127
  time to fit residues: 32.1191
Evaluate side-chains
  164 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   96 THR
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   60 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  130 ILE
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 H residue  113 THR
Chi-restraints excluded: chain K residue  211 LYS
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  576 LEU
Chi-restraints excluded: chain K residue  659 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 77 optimal weight:   50.0000
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 102 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 7 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 132 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
D 134 HIS
G  85 GLN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.108040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.072838 restraints weight = 40156.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.073751 restraints weight = 21684.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.074728 restraints weight = 14168.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.074895 restraints weight = 12843.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.074885 restraints weight = 12026.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15075  Z= 0.182
  Angle     :  0.696   8.729  21416  Z= 0.400
  Chirality :  0.047   0.299   2428
  Planarity :  0.004   0.045   1833
  Dihedral  : 29.297 176.122   3977
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.25 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.79 %
    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 are not related in a simple way.
  whole:  0.22 (0.25), residues: 1129
  helix:  1.58 (0.20), residues: 688
  sheet: -2.57 (0.58), residues: 68
  loop : -2.12 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  78 
 TYR   0.012   0.001   TYR G  51 
 PHE   0.016   0.002   PHE K 240 
 TRP   0.011   0.002   TRP K 217 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.18 (15075)
  covalent geometry    : angle       0.69587 /  0.40 (21416)
  hydrogen bonds       : bond        0.06978 /  4.77 (  756)
  hydrogen bonds       : angle       3.86892 /  2.73 ( 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
  194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 GLU cc_start: 0.7902 (tp30) cc_final: 0.7368 (tp30)
REVERT: C   75 LYS cc_start: 0.8515 (mttp) cc_final: 0.8233 (tmtt)
REVERT: C   82 ARG cc_start: 0.8690 (tpt170) cc_final: 0.8453 (tpt170)
REVERT: C   91 ASP cc_start: 0.7917 (t0) cc_final: 0.7567 (t0)
REVERT: D   67 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8454 (m-80)
REVERT: D  118 GLU cc_start: 0.8207 (mp0) cc_final: 0.7919 (mp0)
REVERT: E   54 TYR cc_start: 0.8152 (m-80) cc_final: 0.7819 (m-80)
REVERT: E   77 ASP cc_start: 0.7776 (m-30) cc_final: 0.7480 (t0)
REVERT: H   86 ILE cc_start: 0.9470 (mm) cc_final: 0.9257 (mt)
REVERT: K  212 TRP cc_start: 0.7940 (t-100) cc_final: 0.7608 (t-100)
REVERT: K  296 MET cc_start: 0.8342 (mtp) cc_final: 0.7507 (mmp)
REVERT: K  608 ASN cc_start: 0.7876 (t0) cc_final: 0.7322 (p0)
  outliers start: 28
  outliers final: 17
  residues processed: 189
  average time/residue: 0.1002
  time to fit residues: 28.1485
Evaluate side-chains
  168 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
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 D residue  127 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  576 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 84 optimal weight:   20.0000
   chunk 69 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 122 optimal weight:    9.9990
   chunk 81 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
** 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 = 0.3783 r_free = 0.3783 target = 0.107361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.072014 restraints weight = 40107.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.072942 restraints weight = 21662.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.073772 restraints weight = 14186.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.073913 restraints weight = 13018.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073988 restraints weight = 11965.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  15075  Z= 0.180
  Angle     :  0.671   9.285  21416  Z= 0.384
  Chirality :  0.045   0.286   2428
  Planarity :  0.004   0.053   1833
  Dihedral  : 29.255 179.881   3973
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.30 %
    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 are not related in a simple way.
  whole:  0.78 (0.26), residues: 1129
  helix:  2.01 (0.20), residues: 688
  sheet: -1.96 (0.65), residues: 66
  loop : -1.95 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 579 
 TYR   0.012   0.001   TYR K 253 
 PHE   0.015   0.001   PHE K 240 
 TRP   0.017   0.002   TRP K 265 
 HIS   0.009   0.001   HIS D  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.18 (15075)
  covalent geometry    : angle       0.67130 /  0.38 (21416)
  hydrogen bonds       : bond        0.06442 /  4.39 (  756)
  hydrogen bonds       : angle       3.72769 /  2.63 ( 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
  191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.7648 (mp0) cc_final: 0.7262 (mp0)
REVERT: C   65 GLU cc_start: 0.8189 (tp30) cc_final: 0.7951 (tp30)
REVERT: C   75 LYS cc_start: 0.8540 (mttp) cc_final: 0.8259 (tmtt)
REVERT: C   82 ARG cc_start: 0.8710 (tpt170) cc_final: 0.8321 (tpt170)
REVERT: C   91 ASP cc_start: 0.7943 (t0) cc_final: 0.7412 (t0)
REVERT: D   67 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (m-80)
REVERT: E   54 TYR cc_start: 0.8163 (m-80) cc_final: 0.7827 (m-80)
REVERT: E   73 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6853 (mt-10)
REVERT: G   57 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8295 (tm-30)
REVERT: K  212 TRP cc_start: 0.7856 (t-100) cc_final: 0.7553 (t-100)
REVERT: K  296 MET cc_start: 0.8401 (mtp) cc_final: 0.7522 (mmp)
REVERT: K  608 ASN cc_start: 0.7970 (t0) cc_final: 0.7388 (p0)
  outliers start: 27
  outliers final: 16
  residues processed: 186
  average time/residue: 0.0988
  time to fit residues: 27.0798
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
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 F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  147 THR
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  355 ASP
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  487 ASN
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:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 101 optimal weight:    0.2980
   chunk 133 optimal weight:    9.9990
   chunk 118 optimal weight:    0.0470
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3814 r_free = 0.3814 target = 0.108925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.071997 restraints weight = 39868.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.074157 restraints weight = 20027.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075517 restraints weight = 13511.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.076296 restraints weight = 10933.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.076650 restraints weight = 9838.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  15075  Z= 0.141
  Angle     :  0.622   8.121  21416  Z= 0.358
  Chirality :  0.043   0.285   2428
  Planarity :  0.004   0.051   1833
  Dihedral  : 29.096 177.859   3973
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.81 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.26), residues: 1129
  helix:  2.27 (0.20), residues: 690
  sheet: -1.95 (0.66), residues: 62
  loop : -1.83 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  78 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.013   0.001   PHE K 240 
 TRP   0.014   0.001   TRP K 217 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.14 (15075)
  covalent geometry    : angle       0.62205 /  0.36 (21416)
  hydrogen bonds       : bond        0.05783 /  3.96 (  756)
  hydrogen bonds       : angle       3.45297 /  2.45 ( 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
  194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: C   75 LYS cc_start: 0.8518 (mttp) cc_final: 0.8280 (tmtt)
REVERT: C   82 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8334 (tpt170)
REVERT: C   91 ASP cc_start: 0.7725 (t0) cc_final: 0.7264 (t0)
REVERT: D   67 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8495 (m-80)
REVERT: E   54 TYR cc_start: 0.8191 (m-80) cc_final: 0.7844 (m-80)
REVERT: K  212 TRP cc_start: 0.7912 (t-100) cc_final: 0.7467 (t-100)
REVERT: K  296 MET cc_start: 0.8383 (mtp) cc_final: 0.7536 (mmp)
REVERT: K  575 LYS cc_start: 0.7968 (tmmt) cc_final: 0.7755 (ttpp)
REVERT: K  608 ASN cc_start: 0.7982 (t0) cc_final: 0.7415 (p0)
  outliers start: 27
  outliers final: 15
  residues processed: 184
  average time/residue: 0.1015
  time to fit residues: 27.2569
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  : 0.471 
-------------------------------------------------------------------------------
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   60 LEU
Chi-restraints excluded: chain E residue  112 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 F residue   80 THR
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  365 LEU
Chi-restraints excluded: chain K residue  448 MET
Chi-restraints excluded: chain K residue  576 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 120 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 89 optimal weight:   30.0000
   chunk 112 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0030
   chunk 124 optimal weight:    5.9990
   overall best weight:    2.7996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
B  25 ASN
** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.106524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.070796 restraints weight = 40008.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.071848 restraints weight = 22204.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.072567 restraints weight = 14655.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072733 restraints weight = 13587.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072755 restraints weight = 12631.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  15075  Z= 0.209
  Angle     :  0.670   7.968  21416  Z= 0.377
  Chirality :  0.045   0.284   2428
  Planarity :  0.004   0.047   1833
  Dihedral  : 29.177 173.887   3973
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.25 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.71 %
    Favored  : 79.02 %
  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 are not related in a simple way.
  whole:  1.02 (0.26), residues: 1129
  helix:  2.24 (0.20), residues: 693
  sheet: -1.87 (0.61), residues: 68
  loop : -2.01 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  78 
 TYR   0.010   0.001   TYR D  65 
 PHE   0.014   0.001   PHE E  67 
 TRP   0.012   0.001   TRP K 217 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.21 (15075)
  covalent geometry    : angle       0.67024 /  0.38 (21416)
  hydrogen bonds       : bond        0.06347 /  4.33 (  756)
  hydrogen bonds       : angle       3.61289 /  2.56 ( 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
  186 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.7415 (OUTLIER) cc_final: 0.7078 (t0)
REVERT: C   42 GLU cc_start: 0.7645 (mp0) cc_final: 0.7438 (mp0)
REVERT: C   65 GLU cc_start: 0.8266 (tp30) cc_final: 0.7586 (tp30)
REVERT: C   82 ARG cc_start: 0.8730 (tpt170) cc_final: 0.8388 (tpt170)
REVERT: C   91 ASP cc_start: 0.7784 (t0) cc_final: 0.7270 (t0)
REVERT: D   67 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8508 (m-80)
REVERT: E   54 TYR cc_start: 0.8166 (m-80) cc_final: 0.7738 (m-80)
REVERT: K  212 TRP cc_start: 0.7729 (t-100) cc_final: 0.7458 (t-100)
REVERT: K  296 MET cc_start: 0.8215 (mtp) cc_final: 0.7466 (mmp)
REVERT: K  575 LYS cc_start: 0.8005 (tmmt) cc_final: 0.7786 (ttpp)
REVERT: K  608 ASN cc_start: 0.8062 (t0) cc_final: 0.7424 (p0)
  outliers start: 32
  outliers final: 22
  residues processed: 176
  average time/residue: 0.1032
  time to fit residues: 26.6098
Evaluate side-chains
  172 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   25 ASN
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 D residue  147 THR
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   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  260 SER
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  487 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 79 optimal weight:   40.0000
   chunk 104 optimal weight:    6.9990
   chunk 131 optimal weight:   10.0000
   chunk 37 optimal weight:    0.6980
   chunk 113 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 105 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 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 = 0.3752 r_free = 0.3752 target = 0.105347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.068892 restraints weight = 39694.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.070532 restraints weight = 21938.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071178 restraints weight = 14531.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.071518 restraints weight = 12467.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.071545 restraints weight = 12020.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  15075  Z= 0.246
  Angle     :  0.714   9.466  21416  Z= 0.397
  Chirality :  0.046   0.290   2428
  Planarity :  0.004   0.056   1833
  Dihedral  : 29.211 170.503   3973
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.40 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.63 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.25), residues: 1129
  helix:  2.06 (0.20), residues: 693
  sheet: -1.64 (0.62), residues: 56
  loop : -2.12 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  78 
 TYR   0.012   0.001   TYR B  72 
 PHE   0.014   0.002   PHE E  67 
 TRP   0.022   0.002   TRP K 217 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00527 /  0.25 (15075)
  covalent geometry    : angle       0.71412 /  0.40 (21416)
  hydrogen bonds       : bond        0.06692 /  4.54 (  756)
  hydrogen bonds       : angle       3.73450 /  2.64 ( 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
  185 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 150
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 ARG cc_start: 0.8738 (tpt170) cc_final: 0.8403 (tpt170)
REVERT: C   91 ASP cc_start: 0.7882 (t0) cc_final: 0.7322 (t0)
REVERT: D   67 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (m-80)
REVERT: D  118 GLU cc_start: 0.8435 (mp0) cc_final: 0.8161 (mm-30)
REVERT: E   54 TYR cc_start: 0.8243 (m-80) cc_final: 0.7811 (m-80)
REVERT: K  212 TRP cc_start: 0.7761 (t-100) cc_final: 0.7496 (t-100)
REVERT: K  296 MET cc_start: 0.8247 (mtp) cc_final: 0.7472 (mmp)
REVERT: K  608 ASN cc_start: 0.8147 (t0) cc_final: 0.7495 (p0)
  outliers start: 35
  outliers final: 29
  residues processed: 173
  average time/residue: 0.1037
  time to fit residues: 26.4698
Evaluate side-chains
  172 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   71 THR
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 D residue  127 LEU
Chi-restraints excluded: chain D residue  147 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  130 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 F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
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 H residue  113 THR
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain K residue  210 VAL
Chi-restraints excluded: chain K residue  260 SER
Chi-restraints excluded: chain K residue  280 ILE
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  346 LEU
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 122 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 129 optimal weight:    1.9990
   chunk 77 optimal weight:   50.0000
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0170
   overall best weight:    1.5424

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
B  25 ASN
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 206 GLN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.106734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.070523 restraints weight = 39824.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.072321 restraints weight = 20498.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.072895 restraints weight = 13513.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.073238 restraints weight = 12026.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.073226 restraints weight = 11680.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15075  Z= 0.158
  Angle     :  0.646   8.322  21416  Z= 0.365
  Chirality :  0.043   0.277   2428
  Planarity :  0.004   0.056   1833
  Dihedral  : 29.050 168.429   3973
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.16 %
    Favored  : 77.48 %
  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 are not related in a simple way.
  whole:  1.15 (0.26), residues: 1129
  helix:  2.31 (0.20), residues: 691
  sheet: -1.38 (0.64), residues: 56
  loop : -1.96 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  78 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.011   0.001   PHE K 240 
 TRP   0.016   0.002   TRP K 217 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.16 (15075)
  covalent geometry    : angle       0.64589 /  0.37 (21416)
  hydrogen bonds       : bond        0.05876 /  3.98 (  756)
  hydrogen bonds       : angle       3.51167 /  2.49 ( 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
  173 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8583 (tt0) cc_final: 0.8269 (tt0)
REVERT: C   65 GLU cc_start: 0.8393 (tp30) cc_final: 0.7840 (tp30)
REVERT: C   82 ARG cc_start: 0.8727 (tpt170) cc_final: 0.8429 (tpt170)
REVERT: C   91 ASP cc_start: 0.7765 (t0) cc_final: 0.7234 (t0)
REVERT: D   67 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8559 (m-80)
REVERT: D  118 GLU cc_start: 0.8444 (mp0) cc_final: 0.8162 (mm-30)
REVERT: E   54 TYR cc_start: 0.8221 (m-80) cc_final: 0.7800 (m-80)
REVERT: H  138 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: K  212 TRP cc_start: 0.7835 (t-100) cc_final: 0.7544 (t-100)
REVERT: K  296 MET cc_start: 0.8217 (mtp) cc_final: 0.7485 (mmp)
REVERT: K  608 ASN cc_start: 0.8229 (t0) cc_final: 0.7428 (p0)
  outliers start: 23
  outliers final: 16
  residues processed: 166
  average time/residue: 0.1002
  time to fit residues: 24.6643
Evaluate side-chains
  159 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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   89 SER
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  112 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 F residue   80 THR
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
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  487 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 67 optimal weight:   30.0000
   chunk 120 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:   50.0000
   chunk 130 optimal weight:   20.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  88 ASN
** K 206 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 = 0.3746 r_free = 0.3746 target = 0.104924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.069248 restraints weight = 39863.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.070201 restraints weight = 21841.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.070850 restraints weight = 14663.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071080 restraints weight = 13605.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071107 restraints weight = 12652.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  15075  Z= 0.239
  Angle     :  0.711   9.537  21416  Z= 0.394
  Chirality :  0.046   0.329   2428
  Planarity :  0.005   0.051   1833
  Dihedral  : 29.110 165.109   3973
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.49 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.86 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1129
  helix:  2.11 (0.20), residues: 692
  sheet: -1.25 (0.66), residues: 56
  loop : -2.11 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  30 
 TYR   0.012   0.001   TYR B  72 
 PHE   0.014   0.002   PHE E  67 
 TRP   0.016   0.002   TRP K 217 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.24 (15075)
  covalent geometry    : angle       0.71111 /  0.39 (21416)
  hydrogen bonds       : bond        0.06598 /  4.48 (  756)
  hydrogen bonds       : angle       3.72592 /  2.64 ( 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
  165 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8634 (tt0) cc_final: 0.8366 (tt0)
REVERT: C   65 GLU cc_start: 0.8367 (tp30) cc_final: 0.7857 (tp30)
REVERT: C   82 ARG cc_start: 0.8764 (tpt170) cc_final: 0.8450 (tpt170)
REVERT: D   67 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8467 (m-80)
REVERT: D  118 GLU cc_start: 0.8575 (mp0) cc_final: 0.8288 (mm-30)
REVERT: E   54 TYR cc_start: 0.8242 (m-80) cc_final: 0.7767 (m-80)
REVERT: H  138 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8224 (mm-30)
REVERT: K  212 TRP cc_start: 0.7729 (t-100) cc_final: 0.7449 (t-100)
REVERT: K  296 MET cc_start: 0.8219 (mtp) cc_final: 0.7499 (mmp)
REVERT: K  448 MET cc_start: 0.8289 (ptp) cc_final: 0.8010 (ptp)
REVERT: K  608 ASN cc_start: 0.8254 (t0) cc_final: 0.7496 (p0)
  outliers start: 23
  outliers final: 21
  residues processed: 161
  average time/residue: 0.1011
  time to fit residues: 24.3156
Evaluate side-chains
  162 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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   60 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  130 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 F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
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  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 42 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 206 GLN
** 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 = 0.3782 r_free = 0.3782 target = 0.107139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.071263 restraints weight = 39634.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.073108 restraints weight = 20431.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.073582 restraints weight = 13450.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.074029 restraints weight = 11782.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073962 restraints weight = 11502.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15075  Z= 0.144
  Angle     :  0.650  11.975  21416  Z= 0.366
  Chirality :  0.043   0.301   2428
  Planarity :  0.004   0.048   1833
  Dihedral  : 28.940 164.663   3973
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 20.57 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.26), residues: 1129
  helix:  2.38 (0.20), residues: 690
  sheet: -1.13 (0.66), residues: 56
  loop : -1.95 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  78 
 TYR   0.011   0.001   TYR G  51 
 PHE   0.012   0.001   PHE K 240 
 TRP   0.015   0.001   TRP K 217 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.14 (15075)
  covalent geometry    : angle       0.65009 /  0.37 (21416)
  hydrogen bonds       : bond        0.05603 /  3.79 (  756)
  hydrogen bonds       : angle       3.47269 /  2.47 ( 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  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8585 (tt0) cc_final: 0.8302 (tt0)
REVERT: C   65 GLU cc_start: 0.8385 (tp30) cc_final: 0.7850 (tp30)
REVERT: C   82 ARG cc_start: 0.8696 (tpt170) cc_final: 0.8396 (tpt170)
REVERT: C   91 ASP cc_start: 0.7966 (t0) cc_final: 0.7245 (t0)
REVERT: D   67 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (m-80)
REVERT: D  118 GLU cc_start: 0.8455 (mp0) cc_final: 0.8146 (mm-30)
REVERT: E   54 TYR cc_start: 0.8185 (m-80) cc_final: 0.7731 (m-80)
REVERT: E  118 THR cc_start: 0.9301 (m) cc_final: 0.8911 (p)
REVERT: G   78 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8147 (mtp-110)
REVERT: K  212 TRP cc_start: 0.7863 (t-100) cc_final: 0.7573 (t-100)
REVERT: K  296 MET cc_start: 0.8186 (mtp) cc_final: 0.7570 (mmp)
REVERT: K  608 ASN cc_start: 0.8270 (t0) cc_final: 0.7485 (p0)
  outliers start: 16
  outliers final: 14
  residues processed: 164
  average time/residue: 0.1017
  time to fit residues: 24.5839
Evaluate side-chains
  159 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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   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   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  365 LEU
Chi-restraints excluded: chain K residue  487 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 118 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.106560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.070625 restraints weight = 39824.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.072245 restraints weight = 21500.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.072853 restraints weight = 14435.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.072956 restraints weight = 12863.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.073042 restraints weight = 12299.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.5410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15075  Z= 0.156
  Angle     :  0.648  12.301  21416  Z= 0.362
  Chirality :  0.043   0.289   2428
  Planarity :  0.004   0.047   1833
  Dihedral  : 28.927 162.607   3973
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.23 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 20.37 %
    Favored  : 77.99 %
  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 are not related in a simple way.
  whole:  1.29 (0.26), residues: 1129
  helix:  2.41 (0.20), residues: 692
  sheet: -1.06 (0.67), residues: 56
  loop : -1.93 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  30 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.043   0.001   PHE K 240 
 TRP   0.015   0.002   TRP K 217 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.16 (15075)
  covalent geometry    : angle       0.64752 /  0.36 (21416)
  hydrogen bonds       : bond        0.05664 /  3.84 (  756)
  hydrogen bonds       : angle       3.47455 /  2.47 ( 1990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1949.54 seconds
wall clock time: 34 minutes 20.30 seconds (2060.30 seconds total)