Starting phenix.real_space_refine
on Fri May 16 04:23:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wh8_37533/05_2025/8wh8_37533.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.52, per 1000 atoms: 0.67
  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: 3.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 5.89
  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: 5.97

  Time building geometry restraints manager: 3.95 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3714
        2.82 -     3.34: 13538
        3.34 -     3.86: 25280
        3.86 -     4.38: 30863
        4.38 -     4.90: 43590
  Nonbonded interactions: 116985
  Sorted by model distance:
  nonbonded pdb=" CG2 VAL K 516 "
            pdb=" CG1 ILE K 519 "
     model   vdw
     2.300 3.860
  nonbonded pdb=" CD1 ILE B  50 "
            pdb=" CG2 ILE E 119 "
     model   vdw
     2.307 3.880
  nonbonded pdb=" O   SER K 547 "
            pdb=" OG1 THR K 600 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OD1 ASN K 368 "
            pdb=" N   SER K 370 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   ASN K 466 "
            pdb=" OG1 THR K 467 "
     model   vdw
     2.325 3.040
  ... (remaining 116980 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 50 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 100)
  selection = (chain 'F' and resid 25 through 100)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 21 through 108)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     38.170
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.060
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.109  15075  Z= 0.821
  Angle     :  1.397  15.230  21416  Z= 0.972
  Chirality :  0.071   0.738   2428
  Planarity :  0.008   0.047   1833
  Dihedral  : 25.117 168.290   6268
  Min Nonbonded Distance : 2.300

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.038   0.003   TRP K 217 
 HIS   0.016   0.002   HIS H  74 
 PHE   0.028   0.003   PHE D  67 
 TYR   0.040   0.003   TYR K 329 
 ARG   0.006   0.001   ARG K 430 

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

*********************** 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  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.6445 (m110) cc_final: 0.5761 (m-40)
REVERT: C   65 GLU cc_start: 0.7509 (tp30) cc_final: 0.7297 (tp30)
REVERT: C   75 LYS cc_start: 0.8499 (mttp) cc_final: 0.8234 (tmtt)
REVERT: E   54 TYR cc_start: 0.8331 (m-80) cc_final: 0.7823 (m-80)
REVERT: E  123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8733 (m-30)
REVERT: F   52 GLU cc_start: 0.7781 (tp30) cc_final: 0.7317 (tp30)
REVERT: G   36 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8702 (mtpt)
REVERT: H  113 THR cc_start: 0.9186 (m) cc_final: 0.8891 (p)
REVERT: H  141 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (mtmt)
REVERT: K  269 ILE cc_start: 0.8514 (tt) cc_final: 0.8306 (mt)
REVERT: K  296 MET cc_start: 0.8179 (mtp) cc_final: 0.7514 (mmp)
REVERT: K  432 MET cc_start: 0.6988 (mmm) cc_final: 0.6731 (tpt)
REVERT: K  446 ILE cc_start: 0.7555 (mt) cc_final: 0.7058 (tp)
REVERT: K  452 MET cc_start: 0.7877 (ttp) cc_final: 0.7651 (ttt)
REVERT: K  626 MET cc_start: 0.8521 (mmt) cc_final: 0.8311 (mmm)
REVERT: K  667 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6737 (mptt)
REVERT: K  669 GLU cc_start: 0.8623 (tp30) cc_final: 0.8340 (tp30)
  outliers start: 7
  outliers final: 1
  residues processed: 328
  average time/residue: 0.3612
  time to fit residues: 155.9177
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
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 113 optimal weight:    0.0000
   chunk 101 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   chunk 40 optimal weight:   20.0000
   chunk 63 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.0588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  93 GLN
D 134 HIS
K 206 GLN
K 286 ASN
K 366 GLN
** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3845 r_free = 0.3845 target = 0.111318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.076985 restraints weight = 39918.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.077958 restraints weight = 20298.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.078687 restraints weight = 13726.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15075  Z= 0.182
  Angle     :  0.663  10.272  21416  Z= 0.379
  Chirality :  0.039   0.155   2428
  Planarity :  0.005   0.038   1833
  Dihedral  : 29.035 173.998   3977
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.34 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.12 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1129
  helix:  1.17 (0.20), residues: 688
  sheet: -2.70 (0.60), residues: 61
  loop : -2.14 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP K 265 
 HIS   0.008   0.001   HIS F  75 
 PHE   0.021   0.002   PHE H  67 
 TYR   0.012   0.001   TYR G  51 
 ARG   0.004   0.001   ARG K 636 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06317 (  756)
  hydrogen bonds       : angle       3.73180 ( 1990)
  covalent geometry    : bond        0.00394 (15075)
  covalent geometry    : angle       0.66278 (21416)

*********************** 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
  220 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.8075 (tp30) cc_final: 0.7872 (mp0)
REVERT: C   65 GLU cc_start: 0.7839 (tp30) cc_final: 0.7449 (tp30)
REVERT: C   75 LYS cc_start: 0.8715 (mttp) cc_final: 0.8278 (tmtt)
REVERT: C   82 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8400 (tpt170)
REVERT: C   85 GLN cc_start: 0.8853 (tp40) cc_final: 0.8648 (tp40)
REVERT: C   91 ASP cc_start: 0.7498 (t0) cc_final: 0.7217 (t0)
REVERT: D   67 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (m-80)
REVERT: D  118 GLU cc_start: 0.8391 (mp0) cc_final: 0.8126 (mp0)
REVERT: E   54 TYR cc_start: 0.8093 (m-80) cc_final: 0.7859 (m-80)
REVERT: G   36 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8730 (ttmm)
REVERT: H   84 MET cc_start: 0.8303 (mtm) cc_final: 0.8068 (mtm)
REVERT: K  296 MET cc_start: 0.8220 (mtp) cc_final: 0.7533 (mmp)
REVERT: K  516 VAL cc_start: 0.8125 (t) cc_final: 0.7904 (t)
REVERT: K  570 ILE cc_start: 0.9104 (pt) cc_final: 0.8617 (mp)
REVERT: K  608 ASN cc_start: 0.7791 (t0) cc_final: 0.7138 (p0)
REVERT: K  626 MET cc_start: 0.8670 (mmt) cc_final: 0.8439 (mmt)
  outliers start: 24
  outliers final: 12
  residues processed: 211
  average time/residue: 0.2679
  time to fit residues: 81.3639
Evaluate side-chains
  166 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   86 SER
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 K residue  210 VAL
Chi-restraints excluded: chain K residue  300 VAL
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  631 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  85 GLN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.110041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.073518 restraints weight = 39719.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.075691 restraints weight = 19920.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.077052 restraints weight = 13417.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.165
  Angle     :  0.605  13.309  21416  Z= 0.342
  Chirality :  0.037   0.273   2428
  Planarity :  0.004   0.035   1833
  Dihedral  : 28.683 178.846   3973
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.43 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.26), residues: 1129
  helix:  1.99 (0.20), residues: 695
  sheet: -2.21 (0.65), residues: 60
  loop : -1.91 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP K 217 
 HIS   0.009   0.001   HIS F  75 
 PHE   0.018   0.001   PHE H  67 
 TYR   0.010   0.001   TYR G  51 
 ARG   0.005   0.000   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05408 (  756)
  hydrogen bonds       : angle       3.44038 ( 1990)
  covalent geometry    : bond        0.00360 (15075)
  covalent geometry    : angle       0.60512 (21416)

*********************** 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
  203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7865 (mp0)
REVERT: C   75 LYS cc_start: 0.8629 (mttp) cc_final: 0.8355 (tmtt)
REVERT: C   78 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6511 (mtt-85)
REVERT: C   82 ARG cc_start: 0.8685 (tpt170) cc_final: 0.8333 (tpt170)
REVERT: C   91 ASP cc_start: 0.7557 (t0) cc_final: 0.7269 (t0)
REVERT: D   67 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8413 (m-80)
REVERT: E   54 TYR cc_start: 0.8195 (m-80) cc_final: 0.7752 (m-80)
REVERT: G   57 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: G   74 ASN cc_start: 0.8788 (m-40) cc_final: 0.7840 (t0)
REVERT: H   86 ILE cc_start: 0.9397 (mm) cc_final: 0.9119 (mt)
REVERT: K  212 TRP cc_start: 0.7924 (t-100) cc_final: 0.7524 (t-100)
REVERT: K  296 MET cc_start: 0.8491 (mtp) cc_final: 0.7605 (mmp)
REVERT: K  448 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (ptp)
REVERT: K  486 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8549 (mm)
REVERT: K  608 ASN cc_start: 0.7962 (t0) cc_final: 0.7336 (p0)
REVERT: K  626 MET cc_start: 0.8583 (mmt) cc_final: 0.8346 (mmm)
  outliers start: 28
  outliers final: 15
  residues processed: 194
  average time/residue: 0.2666
  time to fit residues: 74.0222
Evaluate side-chains
  175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   76 ASP
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  448 MET
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  486 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 94 optimal weight:    0.0870
   chunk 44 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 133 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 110 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0020
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.1768

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
G  85 GLN
K 287 GLN
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 625 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.109260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.073416 restraints weight = 39561.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.075293 restraints weight = 21339.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.076029 restraints weight = 13542.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15075  Z= 0.159
  Angle     :  0.580   8.557  21416  Z= 0.330
  Chirality :  0.036   0.149   2428
  Planarity :  0.004   0.034   1833
  Dihedral  : 28.529 173.823   3973
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.63 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.76 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.26), residues: 1129
  helix:  2.22 (0.20), residues: 700
  sheet: -2.06 (0.62), residues: 60
  loop : -1.89 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K 265 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.014   0.001   PHE H  67 
 TYR   0.010   0.001   TYR D  65 
 ARG   0.013   0.000   ARG K 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05050 (  756)
  hydrogen bonds       : angle       3.26863 ( 1990)
  covalent geometry    : bond        0.00348 (15075)
  covalent geometry    : angle       0.58003 (21416)

*********************** 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
  205 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.7737 (mtm) cc_final: 0.7467 (mtt)
REVERT: C   42 GLU cc_start: 0.7677 (mp0) cc_final: 0.7333 (mp0)
REVERT: C   65 GLU cc_start: 0.8365 (tp30) cc_final: 0.7693 (tp30)
REVERT: C   75 LYS cc_start: 0.8680 (mttp) cc_final: 0.8292 (tptp)
REVERT: C   78 ARG cc_start: 0.6932 (ttm-80) cc_final: 0.6478 (mtt-85)
REVERT: C   82 ARG cc_start: 0.8664 (tpt170) cc_final: 0.8442 (tpt170)
REVERT: C   91 ASP cc_start: 0.7661 (t0) cc_final: 0.7352 (t0)
REVERT: D   67 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8388 (m-80)
REVERT: D  118 GLU cc_start: 0.8531 (mp0) cc_final: 0.8214 (mp0)
REVERT: E   54 TYR cc_start: 0.8095 (m-80) cc_final: 0.7564 (m-80)
REVERT: E   56 LYS cc_start: 0.6735 (pttt) cc_final: 0.5797 (tppt)
REVERT: G   57 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: G   74 ASN cc_start: 0.8770 (m-40) cc_final: 0.7883 (t0)
REVERT: H   86 ILE cc_start: 0.9400 (mm) cc_final: 0.9146 (mt)
REVERT: K  212 TRP cc_start: 0.7769 (t-100) cc_final: 0.7526 (t-100)
REVERT: K  296 MET cc_start: 0.8298 (mtp) cc_final: 0.7529 (mmp)
REVERT: K  366 GLN cc_start: 0.8353 (mt0) cc_final: 0.8010 (mt0)
REVERT: K  608 ASN cc_start: 0.8088 (t0) cc_final: 0.7385 (p0)
REVERT: K  622 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.8346 (m-10)
REVERT: K  626 MET cc_start: 0.8654 (mmt) cc_final: 0.8042 (mmm)
  outliers start: 32
  outliers final: 23
  residues processed: 194
  average time/residue: 0.2635
  time to fit residues: 74.4310
Evaluate side-chains
  182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
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   60 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   73 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 K residue  210 VAL
Chi-restraints excluded: chain K residue  241 LEU
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  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 132 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0070
   chunk 120 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.5202

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

Flipped N/Q/H residues before XYZ refinement:
D 120 GLN
D 134 HIS
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.108198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.072812 restraints weight = 39884.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.074124 restraints weight = 21826.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.074599 restraints weight = 14864.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.171
  Angle     :  0.584   7.437  21416  Z= 0.331
  Chirality :  0.036   0.266   2428
  Planarity :  0.004   0.033   1833
  Dihedral  : 28.463 170.396   3973
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1129
  helix:  2.27 (0.20), residues: 699
  sheet: -1.76 (0.62), residues: 60
  loop : -1.90 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K 217 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.011   0.001   PHE H  67 
 TYR   0.010   0.001   TYR D  65 
 ARG   0.006   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05184 (  756)
  hydrogen bonds       : angle       3.24020 ( 1990)
  covalent geometry    : bond        0.00380 (15075)
  covalent geometry    : angle       0.58447 (21416)

*********************** 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
  192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: C   65 GLU cc_start: 0.8317 (tp30) cc_final: 0.7508 (tp30)
REVERT: C   75 LYS cc_start: 0.8660 (mttp) cc_final: 0.8349 (tptp)
REVERT: C   78 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6577 (mtt-85)
REVERT: C   82 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8480 (tpt170)
REVERT: C   91 ASP cc_start: 0.7613 (t0) cc_final: 0.7276 (t0)
REVERT: D   67 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8405 (m-80)
REVERT: E   54 TYR cc_start: 0.8121 (m-80) cc_final: 0.7573 (m-80)
REVERT: E   56 LYS cc_start: 0.6801 (pttt) cc_final: 0.5889 (tppt)
REVERT: G   57 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: G   74 ASN cc_start: 0.8802 (m-40) cc_final: 0.7909 (t0)
REVERT: G   78 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8207 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8319 (m-40)
REVERT: H   86 ILE cc_start: 0.9482 (mm) cc_final: 0.9212 (mt)
REVERT: K  212 TRP cc_start: 0.7684 (t-100) cc_final: 0.7419 (t-100)
REVERT: K  296 MET cc_start: 0.8202 (mtp) cc_final: 0.7589 (mmp)
REVERT: K  483 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7546 (pttm)
REVERT: K  608 ASN cc_start: 0.8201 (t0) cc_final: 0.7465 (p0)
REVERT: K  622 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.8267 (m-10)
  outliers start: 33
  outliers final: 25
  residues processed: 185
  average time/residue: 0.2637
  time to fit residues: 70.8258
Evaluate side-chains
  175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   62 LEU
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   60 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  112 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 G residue   65 GLU
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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  329 TYR
Chi-restraints excluded: chain K residue  365 LEU
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.5986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.107506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.072475 restraints weight = 39854.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.073226 restraints weight = 22460.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.074102 restraints weight = 15473.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.172
  Angle     :  0.581   7.572  21416  Z= 0.330
  Chirality :  0.036   0.188   2428
  Planarity :  0.004   0.032   1833
  Dihedral  : 28.388 168.034   3973
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 16.58 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1129
  helix:  2.32 (0.20), residues: 699
  sheet: -1.69 (0.64), residues: 62
  loop : -1.80 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 265 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.008   0.001   PHE H  67 
 TYR   0.010   0.001   TYR G  51 
 ARG   0.002   0.000   ARG K 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05157 (  756)
  hydrogen bonds       : angle       3.23148 ( 1990)
  covalent geometry    : bond        0.00384 (15075)
  covalent geometry    : angle       0.58051 (21416)

*********************** 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
  196 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: C   65 GLU cc_start: 0.8393 (tp30) cc_final: 0.7653 (tp30)
REVERT: C   75 LYS cc_start: 0.8601 (mttp) cc_final: 0.8379 (tptp)
REVERT: C   78 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6617 (mtt-85)
REVERT: C   82 ARG cc_start: 0.8620 (tpt170) cc_final: 0.8387 (tpt170)
REVERT: D   67 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8434 (m-80)
REVERT: E   54 TYR cc_start: 0.8259 (m-80) cc_final: 0.7704 (m-80)
REVERT: E   56 LYS cc_start: 0.6861 (pttt) cc_final: 0.5961 (tppt)
REVERT: E   60 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7520 (mp)
REVERT: G   57 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8433 (tm-30)
REVERT: G   73 ASP cc_start: 0.8613 (m-30) cc_final: 0.7873 (t0)
REVERT: G   74 ASN cc_start: 0.8811 (m-40) cc_final: 0.7836 (t0)
REVERT: G   78 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8175 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8232 (m-40)
REVERT: H   86 ILE cc_start: 0.9486 (mm) cc_final: 0.9225 (mt)
REVERT: K  212 TRP cc_start: 0.7769 (t-100) cc_final: 0.7475 (t-100)
REVERT: K  296 MET cc_start: 0.8154 (mtp) cc_final: 0.7559 (mmp)
REVERT: K  608 ASN cc_start: 0.8254 (t0) cc_final: 0.7556 (p0)
REVERT: K  622 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (m-10)
  outliers start: 41
  outliers final: 26
  residues processed: 187
  average time/residue: 0.2672
  time to fit residues: 71.9117
Evaluate side-chains
  178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   62 LEU
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   86 SER
Chi-restraints excluded: chain E residue  112 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 G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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  436 VAL
Chi-restraints excluded: chain K residue  483 LYS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  622 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 108 optimal weight:    0.0060
   chunk 61 optimal weight:    2.9990
   chunk 126 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 133 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 287 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 = 0.3798 r_free = 0.3798 target = 0.107681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.072618 restraints weight = 40011.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.073463 restraints weight = 21589.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.074397 restraints weight = 14462.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.162
  Angle     :  0.571   6.666  21416  Z= 0.324
  Chirality :  0.035   0.197   2428
  Planarity :  0.004   0.032   1833
  Dihedral  : 28.319 167.507   3973
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.68 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1129
  helix:  2.38 (0.20), residues: 704
  sheet: -1.48 (0.60), residues: 68
  loop : -1.96 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 265 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.013   0.001   PHE K 240 
 TYR   0.023   0.001   TYR K 618 
 ARG   0.003   0.000   ARG K 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04929 (  756)
  hydrogen bonds       : angle       3.16928 ( 1990)
  covalent geometry    : bond        0.00358 (15075)
  covalent geometry    : angle       0.57092 (21416)

*********************** 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
  183 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8378 (tm-30)
REVERT: C   42 GLU cc_start: 0.7688 (mp0) cc_final: 0.7469 (mp0)
REVERT: C   65 GLU cc_start: 0.8409 (tp30) cc_final: 0.7677 (tp30)
REVERT: C   78 ARG cc_start: 0.7049 (ttm-80) cc_final: 0.6514 (mtt-85)
REVERT: C   82 ARG cc_start: 0.8630 (tpt170) cc_final: 0.8396 (tpt170)
REVERT: C   91 ASP cc_start: 0.7890 (t0) cc_final: 0.7628 (t0)
REVERT: D   67 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (m-80)
REVERT: E   54 TYR cc_start: 0.8170 (m-80) cc_final: 0.7512 (m-80)
REVERT: E   56 LYS cc_start: 0.6918 (pttt) cc_final: 0.5962 (tppt)
REVERT: E   60 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7465 (mp)
REVERT: G   57 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8448 (tm-30)
REVERT: G   73 ASP cc_start: 0.8637 (m-30) cc_final: 0.7921 (t0)
REVERT: G   74 ASN cc_start: 0.8792 (m-40) cc_final: 0.7862 (t0)
REVERT: G   78 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8100 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8203 (m-40)
REVERT: H   86 ILE cc_start: 0.9472 (mm) cc_final: 0.9207 (mt)
REVERT: K  212 TRP cc_start: 0.7796 (t-100) cc_final: 0.7501 (t-100)
REVERT: K  296 MET cc_start: 0.8157 (mtp) cc_final: 0.7613 (mmp)
REVERT: K  354 MET cc_start: 0.7544 (mtm) cc_final: 0.6994 (mtm)
REVERT: K  608 ASN cc_start: 0.8242 (t0) cc_final: 0.7594 (p0)
  outliers start: 30
  outliers final: 23
  residues processed: 177
  average time/residue: 0.2665
  time to fit residues: 68.6845
Evaluate side-chains
  174 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   62 LEU
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   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   80 VAL
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.108274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.071549 restraints weight = 39796.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073576 restraints weight = 20990.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.074865 restraints weight = 14473.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.5987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15075  Z= 0.152
  Angle     :  0.573   8.784  21416  Z= 0.322
  Chirality :  0.035   0.164   2428
  Planarity :  0.003   0.032   1833
  Dihedral  : 28.254 166.076   3973
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1129
  helix:  2.39 (0.20), residues: 711
  sheet: -0.91 (0.64), residues: 56
  loop : -2.00 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K 265 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.022   0.001   PHE K 240 
 TYR   0.014   0.001   TYR K 618 
 ARG   0.002   0.000   ARG K 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04732 (  756)
  hydrogen bonds       : angle       3.08630 ( 1990)
  covalent geometry    : bond        0.00334 (15075)
  covalent geometry    : angle       0.57328 (21416)

*********************** 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
  190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: C   42 GLU cc_start: 0.7677 (mp0) cc_final: 0.7447 (mp0)
REVERT: C   65 GLU cc_start: 0.8453 (tp30) cc_final: 0.7736 (tp30)
REVERT: C   78 ARG cc_start: 0.6998 (ttm-80) cc_final: 0.6506 (mtt-85)
REVERT: D   67 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8490 (m-80)
REVERT: E   56 LYS cc_start: 0.7047 (pttt) cc_final: 0.6089 (tppt)
REVERT: E   60 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7460 (mp)
REVERT: G   57 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8405 (tm-30)
REVERT: G   73 ASP cc_start: 0.8560 (m-30) cc_final: 0.7839 (t0)
REVERT: G   74 ASN cc_start: 0.8742 (m-40) cc_final: 0.7881 (t0)
REVERT: G   78 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8077 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8272 (m-40)
REVERT: H   86 ILE cc_start: 0.9461 (mm) cc_final: 0.9202 (mt)
REVERT: K  212 TRP cc_start: 0.7828 (t-100) cc_final: 0.7540 (t-100)
REVERT: K  296 MET cc_start: 0.8155 (mtp) cc_final: 0.7721 (mmp)
REVERT: K  608 ASN cc_start: 0.8317 (t0) cc_final: 0.7720 (p0)
  outliers start: 31
  outliers final: 23
  residues processed: 182
  average time/residue: 0.2773
  time to fit residues: 72.5186
Evaluate side-chains
  178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 LEU
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   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   85 GLN
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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  478 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 37 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  88 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 = 0.3794 r_free = 0.3794 target = 0.107536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.072559 restraints weight = 39546.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073715 restraints weight = 21729.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.074130 restraints weight = 14787.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.6155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.163
  Angle     :  0.585   7.886  21416  Z= 0.329
  Chirality :  0.035   0.167   2428
  Planarity :  0.004   0.039   1833
  Dihedral  : 28.264 163.192   3973
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.78 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.01 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1129
  helix:  2.34 (0.20), residues: 711
  sheet: -0.88 (0.65), residues: 56
  loop : -1.94 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 265 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.027   0.001   PHE K 240 
 TYR   0.033   0.001   TYR K 618 
 ARG   0.002   0.000   ARG K 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04967 (  756)
  hydrogen bonds       : angle       3.17704 ( 1990)
  covalent geometry    : bond        0.00363 (15075)
  covalent geometry    : angle       0.58508 (21416)

*********************** 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
  179 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: C   65 GLU cc_start: 0.8435 (tp30) cc_final: 0.7693 (tp30)
REVERT: C   78 ARG cc_start: 0.7057 (ttm-80) cc_final: 0.6623 (mtt-85)
REVERT: D   67 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8447 (m-80)
REVERT: D  130 GLU cc_start: 0.6327 (tp30) cc_final: 0.6029 (tm-30)
REVERT: E   56 LYS cc_start: 0.7031 (pttt) cc_final: 0.6240 (tptt)
REVERT: E   60 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7654 (mp)
REVERT: G   57 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8442 (tm-30)
REVERT: G   73 ASP cc_start: 0.8566 (m-30) cc_final: 0.7928 (t0)
REVERT: G   74 ASN cc_start: 0.8777 (m-40) cc_final: 0.7894 (t0)
REVERT: G   78 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8027 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8217 (m-40)
REVERT: H   84 MET cc_start: 0.8610 (ttm) cc_final: 0.8391 (tpp)
REVERT: H   86 ILE cc_start: 0.9493 (mm) cc_final: 0.9213 (mt)
REVERT: K  212 TRP cc_start: 0.7651 (t-100) cc_final: 0.7370 (t-100)
REVERT: K  296 MET cc_start: 0.8030 (mtp) cc_final: 0.7726 (mmp)
REVERT: K  354 MET cc_start: 0.7332 (mtm) cc_final: 0.6810 (mtm)
REVERT: K  608 ASN cc_start: 0.8242 (t0) cc_final: 0.7765 (p0)
REVERT: K  631 MET cc_start: 0.8145 (ptp) cc_final: 0.7927 (pmm)
  outliers start: 28
  outliers final: 23
  residues processed: 174
  average time/residue: 0.2678
  time to fit residues: 66.7314
Evaluate side-chains
  168 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 LEU
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 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   80 VAL
Chi-restraints excluded: chain G residue   85 GLN
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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  478 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0030
   chunk 129 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 116 optimal weight:    7.9990
   chunk 56 optimal weight:    0.5980
   chunk 102 optimal weight:    9.9990
   overall best weight:    1.9196

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 539 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.106229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.071152 restraints weight = 39626.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.071855 restraints weight = 22084.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.072698 restraints weight = 15021.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.6284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15075  Z= 0.185
  Angle     :  0.607   8.586  21416  Z= 0.339
  Chirality :  0.036   0.165   2428
  Planarity :  0.004   0.039   1833
  Dihedral  : 28.326 160.141   3973
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.22 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1129
  helix:  2.25 (0.20), residues: 711
  sheet: -0.93 (0.65), residues: 56
  loop : -1.95 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 265 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.032   0.001   PHE K 240 
 TYR   0.028   0.001   TYR K 618 
 ARG   0.003   0.000   ARG K 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  756)
  hydrogen bonds       : angle       3.27198 ( 1990)
  covalent geometry    : bond        0.00417 (15075)
  covalent geometry    : angle       0.60736 (21416)

********************** 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
  176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: C   65 GLU cc_start: 0.8451 (tp30) cc_final: 0.7833 (tp30)
REVERT: C   78 ARG cc_start: 0.7008 (ttm-80) cc_final: 0.6547 (mtt-85)
REVERT: D   67 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8392 (m-80)
REVERT: D  130 GLU cc_start: 0.6417 (tp30) cc_final: 0.6101 (tm-30)
REVERT: E   56 LYS cc_start: 0.7219 (pttt) cc_final: 0.6501 (tptt)
REVERT: G   57 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: G   73 ASP cc_start: 0.8689 (m-30) cc_final: 0.7984 (t0)
REVERT: G   74 ASN cc_start: 0.8872 (m-40) cc_final: 0.7909 (t0)
REVERT: G   78 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8008 (mtp-110)
REVERT: G   90 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8248 (m-40)
REVERT: H   86 ILE cc_start: 0.9520 (mm) cc_final: 0.9240 (mt)
REVERT: K  212 TRP cc_start: 0.7719 (t-100) cc_final: 0.7456 (t-100)
REVERT: K  296 MET cc_start: 0.8126 (mtp) cc_final: 0.7831 (mmp)
REVERT: K  320 ARG cc_start: 0.6448 (tpt170) cc_final: 0.6184 (tpt170)
REVERT: K  354 MET cc_start: 0.7443 (mtm) cc_final: 0.7002 (mtm)
REVERT: K  608 ASN cc_start: 0.8352 (t0) cc_final: 0.7850 (p0)
  outliers start: 26
  outliers final: 21
  residues processed: 171
  average time/residue: 0.2745
  time to fit residues: 67.2336
Evaluate side-chains
  171 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 LEU
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 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   80 VAL
Chi-restraints excluded: chain G residue   85 GLN
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain H residue  113 THR
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  478 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 128 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 108 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
F  75 HIS
** K 539 ASN ** 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 = 0.3757 r_free = 0.3757 target = 0.105204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070214 restraints weight = 39884.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.070885 restraints weight = 22091.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.071733 restraints weight = 15030.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.6431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  15075  Z= 0.210
  Angle     :  0.625   8.713  21416  Z= 0.349
  Chirality :  0.038   0.169   2428
  Planarity :  0.004   0.038   1833
  Dihedral  : 28.391 157.772   3973
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1129
  helix:  2.17 (0.20), residues: 710
  sheet: -0.97 (0.66), residues: 56
  loop : -2.01 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K 265 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.035   0.001   PHE K 240 
 TYR   0.029   0.001   TYR K 618 
 ARG   0.003   0.000   ARG D 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05592 (  756)
  hydrogen bonds       : angle       3.38176 ( 1990)
  covalent geometry    : bond        0.00480 (15075)
  covalent geometry    : angle       0.62533 (21416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4257.37 seconds
wall clock time: 75 minutes 15.77 seconds (4515.77 seconds total)