Starting phenix.real_space_refine
on Mon Apr  6 00:23:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jo9_22408/04_2026/7jo9_22408.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     290      5.49       5
     S      25      5.16       5
     C    8556      2.51       5
     N    2771      2.21       5
     O    3351      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14994
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 683
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 2960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2960
          Classifications: {'peptide': 358}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342}
    Chain: "K"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13969  SG  CYS K 384      40.430  21.150  77.314  1.00 84.47           S
  ATOM  13975  SG  CYS K 385      36.531  21.814  76.213  1.00 87.46           S
  ATOM  14020  SG  CYS K 392      36.749  21.709  79.807  1.00 89.32           S

  Time building chain proxies: 3.23, per 1000 atoms: 0.22
  Number of scatterers: 14994
  At special positions: 0
  Unit cell: (121.03, 135.59, 125.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      25     16.00
     P     290     15.00
     O    3351      8.00
     N    2771      7.00
     C    8556      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 471.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 601 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 385 "
        pdb="ZN    ZN K 601 " - pdb=" NE2 HIS K 378 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 392 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 384 "
      Number of angles added : 3


  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      63.0% alpha, 7.4% beta
      138 base pairs and 252 stacking pairs defined.
    Time for finding SS restraints: 2.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.512A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.530A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.527A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.670A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 4.219A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.500A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.610A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 4.043A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.739A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.629A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.703A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 4.109A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.977A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.596A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.611A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.575A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.102A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.583A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.611A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 4.043A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.739A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.629A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.703A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 4.109A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 149 through 185
      removed outlier: 4.019A  pdb=" N   ARG K 161 " --> pdb=" O   LEU K 157 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   LYS K 162 " --> pdb=" O   ARG K 158 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ASP K 163 " --> pdb=" O   LEU K 159 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE K 164 " --> pdb=" O   LYS K 160 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   GLU K 166 " --> pdb=" O   LYS K 162 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   ALA K 167 " --> pdb=" O   ASP K 163 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 248 through 250
      No H-bonds generated for 'chain 'K' and resid 248 through 250'
    Processing helix  chain 'K' and resid 258 through 276
      removed outlier: 3.741A  pdb=" N   GLU K 276 " --> pdb=" O   GLU K 272 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 319 through 325
      removed outlier: 4.400A  pdb=" N   GLU K 324 " --> pdb=" O   SER K 321 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 333 through 342
      removed outlier: 3.535A  pdb=" N   ARG K 337 " --> pdb=" O   GLY K 333 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 367 through 377
    Processing helix  chain 'K' and resid 393 through 412
    Processing helix  chain 'K' and resid 413 through 416
    Processing helix  chain 'K' and resid 419 through 434
      removed outlier: 3.999A  pdb=" N   VAL K 423 " --> pdb=" O   CYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 436 through 443
      removed outlier: 4.028A  pdb=" N   ASP K 441 " --> pdb=" O   SER K 438 " (cutoff:3.500A)
      Proline residue:  K 442  - end of helix
    Processing helix  chain 'K' and resid 444 through 463
    Processing helix  chain 'K' and resid 482 through 499
    Processing helix  chain 'K' and resid 501 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.137A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.629A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.957A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.489A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.767A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195
      removed outlier: 4.619A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP K 281 " --> pdb=" O   ARG K 299 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195
      removed outlier: 4.619A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   LEU K 310 " --> pdb=" O   PRO K 349 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227
    Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253

    511 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      356 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      252 stacking parallelities
  Total time for adding SS restraints: 3.45

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3006
        1.33 -     1.45: 4768
        1.45 -     1.57: 7469
        1.57 -     1.69: 578
        1.69 -     1.81: 40
  Bond restraints: 15861
  Sorted by residual:
  bond pdb=" C   LEU D 102 "
       pdb=" N   PRO D 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.016 1.11e-02 8.12e+03 2.19e+00
  bond pdb=" C   LEU H 102 "
       pdb=" N   PRO H 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.015 1.11e-02 8.12e+03 1.91e+00
  bond pdb=" CB  LEU D  80 "
       pdb=" CG  LEU D  80 "
    ideal  model  delta    sigma   weight residual
    1.530  1.505  0.025 2.00e-02 2.50e+03 1.59e+00
  bond pdb=" CB  LEU H  80 "
       pdb=" CG  LEU H  80 "
    ideal  model  delta    sigma   weight residual
    1.530  1.505  0.025 2.00e-02 2.50e+03 1.53e+00
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.49e+00
  ... (remaining 15856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 21551
        1.59 -     3.17: 985
        3.17 -     4.76: 69
        4.76 -     6.35: 21
        6.35 -     7.93: 8
  Bond angle restraints: 22634
  Sorted by residual:
  angle pdb=" CA  GLY H  53 "
        pdb=" C   GLY H  53 "
        pdb=" N   ILE H  54 "
      ideal   model   delta    sigma   weight residual
     115.27  117.77   -2.50 7.60e-01 1.73e+00 1.08e+01
  angle pdb=" CA  GLY D  53 "
        pdb=" C   GLY D  53 "
        pdb=" N   ILE D  54 "
      ideal   model   delta    sigma   weight residual
     115.27  117.71   -2.44 7.60e-01 1.73e+00 1.03e+01
  angle pdb=" N   ARG K 222 "
        pdb=" CA  ARG K 222 "
        pdb=" C   ARG K 222 "
      ideal   model   delta    sigma   weight residual
     111.02  114.33   -3.31 1.25e+00 6.40e-01 7.00e+00
  angle pdb=" CB  MET F  84 "
        pdb=" CG  MET F  84 "
        pdb=" SD  MET F  84 "
      ideal   model   delta    sigma   weight residual
     112.70  104.77    7.93 3.00e+00 1.11e-01 6.99e+00
  angle pdb=" C   ARG D  33 "
        pdb=" CA  ARG D  33 "
        pdb=" CB  ARG D  33 "
      ideal   model   delta    sigma   weight residual
     109.80  114.06   -4.26 1.70e+00 3.46e-01 6.29e+00
  ... (remaining 22629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.52: 7314
       33.52 -    67.04: 1488
       67.04 -   100.56: 40
      100.56 -   134.08: 0
      134.08 -   167.60: 1
  Dihedral angle restraints: 8843
    sinusoidal: 5568
      harmonic: 3275
  Sorted by residual:
  dihedral pdb=" CA  ARG H  33 "
           pdb=" C   ARG H  33 "
           pdb=" N   LYS H  34 "
           pdb=" CA  LYS H  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.78  -24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  ARG D  33 "
           pdb=" C   ARG D  33 "
           pdb=" N   LYS D  34 "
           pdb=" CA  LYS D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.79  -24.21     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   52.40  167.60     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 8840 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1386
       0.029 -    0.059: 777
       0.059 -    0.088: 279
       0.088 -    0.117: 80
       0.117 -    0.147: 25
  Chirality restraints: 2547
  Sorted by residual:
  chirality pdb=" CB  ILE H  54 "
            pdb=" CA  ILE H  54 "
            pdb=" CG1 ILE H  54 "
            pdb=" CG2 ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  PRO H  50 "
            pdb=" N   PRO H  50 "
            pdb=" C   PRO H  50 "
            pdb=" CB  PRO H  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 2544 not shown)

  Planarity restraints: 1861
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER K 446 "    0.016 2.00e-02 2.50e+03   3.16e-02 9.99e+00
        pdb=" C   SER K 446 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   SER K 446 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER K 447 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA K 454 "   -0.015 2.00e-02 2.50e+03   3.09e-02 9.54e+00
        pdb=" C   ALA K 454 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ALA K 454 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE K 455 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER K 447 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.61e+00
        pdb=" C   SER K 447 "    0.051 2.00e-02 2.50e+03
        pdb=" O   SER K 447 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   CYS K 448 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1858 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2251
        2.76 -     3.29: 13369
        3.29 -     3.83: 26368
        3.83 -     4.36: 30229
        4.36 -     4.90: 45966
  Nonbonded interactions: 118183
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  64 "
            pdb=" NH2 ARG K 222 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OH  TYR K 421 "
            pdb=" NE2 HIS K 467 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE1 GLU C  92 "
            pdb=" NH1 ARG K 241 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NH2 ARG F  19 "
            pdb=" OP1  DA J -22 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   ARG E 129 "
            pdb=" NH1 ARG E 129 "
     model   vdw
     2.289 3.120
  ... (remaining 118178 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 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 21 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.370
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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      :  0.009   0.437  15865  Z= 0.370
  Angle     :  0.741   7.933  22637  Z= 0.442
  Chirality :  0.042   0.147   2547
  Planarity :  0.005   0.067   1861
  Dihedral  : 25.947 167.599   6725
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.72 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 1107
  helix:  1.48 (0.20), residues: 646
  sheet: -0.28 (0.64), residues: 57
  loop : -1.83 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 443 
 TYR   0.023   0.002   TYR K 346 
 PHE   0.023   0.002   PHE K 266 
 TRP   0.014   0.002   TRP K 363 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00771 (15861)
  covalent geometry    : angle       0.73807 (22634)
  hydrogen bonds       : bond        0.11259 (  864)
  hydrogen bonds       : angle       4.29722 ( 2194)
  metal coordination   : bond        0.26951 (    4)
  metal coordination   : angle       5.96912 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 231
  time to evaluate  : 0.308 
Fit side-chains
REVERT: D   68 ASP cc_start: 0.8115 (t0) cc_final: 0.7913 (t0)
REVERT: E   73 GLU cc_start: 0.8100 (tt0) cc_final: 0.7667 (tt0)
REVERT: E   90 MET cc_start: 0.7432 (mmp) cc_final: 0.7134 (mmm)
REVERT: F   68 ASP cc_start: 0.7764 (m-30) cc_final: 0.7555 (m-30)
REVERT: F   91 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8156 (ttmm)
REVERT: G   99 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8073 (mmtt)
REVERT: K  173 LYS cc_start: 0.5271 (mtmm) cc_final: 0.5067 (mtmt)
REVERT: K  269 ILE cc_start: 0.6058 (mt) cc_final: 0.5368 (tt)
  outliers start: 4
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1754
  time to fit residues: 53.6887
Evaluate side-chains
  134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
D  63 ASN
E  68 GLN
G  38 ASN
K 339 ASN
K 429 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.150271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111831 restraints weight = 22165.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.42
r_work: 0.2908 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15865  Z= 0.177
  Angle     :  0.589   6.588  22637  Z= 0.344
  Chirality :  0.036   0.156   2547
  Planarity :  0.005   0.057   1861
  Dihedral  : 28.740 173.455   4411
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.36 %
    Favored  : 89.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.26), residues: 1107
  helix:  2.39 (0.21), residues: 661
  sheet:  0.28 (0.65), residues: 58
  loop : -1.32 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  42 
 TYR   0.017   0.002   TYR H  83 
 PHE   0.018   0.002   PHE A 104 
 TRP   0.013   0.001   TRP K 363 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (15861)
  covalent geometry    : angle       0.58855 (22634)
  hydrogen bonds       : bond        0.05823 (  864)
  hydrogen bonds       : angle       2.90423 ( 2194)
  metal coordination   : bond        0.01407 (    4)
  metal coordination   : angle       2.84661 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8408 (mtpt)
REVERT: D   33 ARG cc_start: 0.7188 (ppt170) cc_final: 0.6881 (ptt180)
REVERT: D   63 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8274 (m-40)
REVERT: D   68 ASP cc_start: 0.8401 (t0) cc_final: 0.8160 (t70)
REVERT: F   91 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8613 (tttt)
REVERT: G   99 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8477 (mmmt)
REVERT: K  173 LYS cc_start: 0.5054 (mtmm) cc_final: 0.4710 (mtmt)
REVERT: K  180 ARG cc_start: 0.4508 (tpm170) cc_final: 0.3877 (mtm180)
REVERT: K  472 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6579 (ptpp)
REVERT: K  487 GLU cc_start: 0.5512 (mt-10) cc_final: 0.5279 (mt-10)
REVERT: K  496 GLU cc_start: 0.5149 (mm-30) cc_final: 0.4330 (tp30)
REVERT: K  501 PHE cc_start: 0.5177 (m-80) cc_final: 0.4861 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 162
  average time/residue: 0.1627
  time to fit residues: 35.7218
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain K residue  423 VAL
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  458 GLU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 123 optimal weight:    0.0770
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
E  76 GLN
F  75 HIS
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.153705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.116788 restraints weight = 22499.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.49
r_work: 0.2911 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15865  Z= 0.141
  Angle     :  0.513   4.920  22637  Z= 0.306
  Chirality :  0.033   0.126   2547
  Planarity :  0.004   0.045   1861
  Dihedral  : 28.644 173.929   4411
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.63 %
    Favored  : 88.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.26), residues: 1107
  helix:  2.71 (0.20), residues: 663
  sheet:  0.56 (0.68), residues: 58
  loop : -1.17 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  42 
 TYR   0.010   0.001   TYR H  83 
 PHE   0.017   0.001   PHE K 455 
 TRP   0.007   0.001   TRP K 363 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (15861)
  covalent geometry    : angle       0.51235 (22634)
  hydrogen bonds       : bond        0.04640 (  864)
  hydrogen bonds       : angle       2.66370 ( 2194)
  metal coordination   : bond        0.00507 (    4)
  metal coordination   : angle       2.65533 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.370 
Fit side-chains
REVERT: D   63 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8194 (m-40)
REVERT: D   68 ASP cc_start: 0.8337 (t0) cc_final: 0.8091 (t70)
REVERT: F   91 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8600 (tttt)
REVERT: G   99 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8531 (mmmt)
REVERT: K  173 LYS cc_start: 0.5090 (mtmm) cc_final: 0.4777 (mtmt)
REVERT: K  373 TYR cc_start: 0.6230 (t80) cc_final: 0.6011 (t80)
REVERT: K  472 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6739 (ptpp)
REVERT: K  496 GLU cc_start: 0.5371 (mm-30) cc_final: 0.4837 (tp30)
REVERT: K  501 PHE cc_start: 0.5316 (m-80) cc_final: 0.5017 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 142
  average time/residue: 0.1719
  time to fit residues: 32.5985
Evaluate side-chains
  129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 129 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0770
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
D  63 ASN
F  25 ASN
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.153879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.117377 restraints weight = 22342.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.46
r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15865  Z= 0.137
  Angle     :  0.506   5.724  22637  Z= 0.302
  Chirality :  0.033   0.127   2547
  Planarity :  0.004   0.042   1861
  Dihedral  : 28.592 173.998   4411
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.73 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.26), residues: 1107
  helix:  2.84 (0.20), residues: 664
  sheet:  0.69 (0.71), residues: 58
  loop : -1.05 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  42 
 TYR   0.009   0.001   TYR H  83 
 PHE   0.009   0.001   PHE C  25 
 TRP   0.007   0.001   TRP K 363 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (15861)
  covalent geometry    : angle       0.50422 (22634)
  hydrogen bonds       : bond        0.04540 (  864)
  hydrogen bonds       : angle       2.60380 ( 2194)
  metal coordination   : bond        0.00606 (    4)
  metal coordination   : angle       3.59197 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.387 
Fit side-chains
REVERT: D   63 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8203 (m-40)
REVERT: D   68 ASP cc_start: 0.8393 (t0) cc_final: 0.8067 (t70)
REVERT: F   91 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8539 (ttmm)
REVERT: G   99 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8514 (mmmt)
REVERT: K  173 LYS cc_start: 0.5168 (mtmm) cc_final: 0.4861 (mtmt)
REVERT: K  180 ARG cc_start: 0.4534 (tpm170) cc_final: 0.3815 (mtm-85)
REVERT: K  373 TYR cc_start: 0.6219 (t80) cc_final: 0.5659 (t80)
REVERT: K  472 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6781 (ptpp)
REVERT: K  496 GLU cc_start: 0.5439 (mm-30) cc_final: 0.4842 (tp30)
REVERT: K  501 PHE cc_start: 0.5349 (m-80) cc_final: 0.5119 (m-80)
  outliers start: 16
  outliers final: 5
  residues processed: 138
  average time/residue: 0.1662
  time to fit residues: 30.8641
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0010
   chunk 43 optimal weight:    0.0980
   chunk 106 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.154253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117221 restraints weight = 22344.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.48
r_work: 0.2922 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15865  Z= 0.134
  Angle     :  0.500   7.859  22637  Z= 0.296
  Chirality :  0.033   0.124   2547
  Planarity :  0.004   0.039   1861
  Dihedral  : 28.560 174.078   4411
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.87 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.26), residues: 1107
  helix:  2.92 (0.20), residues: 667
  sheet:  1.28 (0.72), residues: 54
  loop : -1.00 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  42 
 TYR   0.007   0.001   TYR H  83 
 PHE   0.015   0.001   PHE K 449 
 TRP   0.006   0.001   TRP K 363 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (15861)
  covalent geometry    : angle       0.49908 (22634)
  hydrogen bonds       : bond        0.04367 (  864)
  hydrogen bonds       : angle       2.54587 ( 2194)
  metal coordination   : bond        0.00401 (    4)
  metal coordination   : angle       2.25920 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.416 
Fit side-chains
REVERT: D   68 ASP cc_start: 0.8375 (t0) cc_final: 0.8049 (t70)
REVERT: F   91 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8592 (ttmm)
REVERT: G   99 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8498 (mmmt)
REVERT: K  373 TYR cc_start: 0.6307 (t80) cc_final: 0.5813 (t80)
REVERT: K  472 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6767 (ptpp)
REVERT: K  496 GLU cc_start: 0.5398 (mm-30) cc_final: 0.4890 (tp30)
  outliers start: 11
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1793
  time to fit residues: 31.8671
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 116 optimal weight:    0.0370
   chunk 82 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.1260

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
E  76 GLN
K 499 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113963 restraints weight = 22173.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.33
r_work: 0.2923 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15865  Z= 0.164
  Angle     :  0.538   9.598  22637  Z= 0.316
  Chirality :  0.035   0.139   2547
  Planarity :  0.004   0.046   1861
  Dihedral  : 28.682 174.569   4411
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.59 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.26), residues: 1107
  helix:  2.77 (0.20), residues: 667
  sheet:  0.66 (0.71), residues: 60
  loop : -0.97 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  42 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.015   0.002   PHE C  25 
 TRP   0.018   0.002   TRP K 431 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (15861)
  covalent geometry    : angle       0.53744 (22634)
  hydrogen bonds       : bond        0.05650 (  864)
  hydrogen bonds       : angle       2.67566 ( 2194)
  metal coordination   : bond        0.00333 (    4)
  metal coordination   : angle       2.16350 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.418 
Fit side-chains
REVERT: D   68 ASP cc_start: 0.8475 (t0) cc_final: 0.8166 (t70)
REVERT: F   91 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8570 (ttmm)
REVERT: G   99 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8539 (mmmt)
REVERT: K  180 ARG cc_start: 0.4611 (tpm170) cc_final: 0.3951 (mtm-85)
REVERT: K  373 TYR cc_start: 0.6433 (t80) cc_final: 0.5904 (t80)
REVERT: K  472 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6891 (ptpp)
REVERT: K  496 GLU cc_start: 0.5424 (mm-30) cc_final: 0.4908 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1701
  time to fit residues: 31.3394
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  446 SER
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 134 optimal weight:    9.9990
   chunk 95 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
F  18 HIS
K 499 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.147013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.108366 restraints weight = 21914.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.45
r_work: 0.2838 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  15865  Z= 0.222
  Angle     :  0.604  10.568  22637  Z= 0.351
  Chirality :  0.038   0.153   2547
  Planarity :  0.005   0.052   1861
  Dihedral  : 28.889 175.032   4411
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.52 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.25), residues: 1107
  helix:  2.40 (0.20), residues: 668
  sheet:  0.60 (0.69), residues: 61
  loop : -1.24 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  42 
 TYR   0.012   0.002   TYR H  83 
 PHE   0.023   0.002   PHE C  25 
 TRP   0.008   0.002   TRP K 431 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (15861)
  covalent geometry    : angle       0.60404 (22634)
  hydrogen bonds       : bond        0.07017 (  864)
  hydrogen bonds       : angle       2.86511 ( 2194)
  metal coordination   : bond        0.00429 (    4)
  metal coordination   : angle       2.10145 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.421 
Fit side-chains
REVERT: F   91 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8615 (ttmm)
REVERT: G   99 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8503 (mmmt)
REVERT: K  180 ARG cc_start: 0.4832 (tpm170) cc_final: 0.4070 (mtm-85)
REVERT: K  431 TRP cc_start: 0.7391 (m-10) cc_final: 0.7140 (m-10)
REVERT: K  472 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7176 (ptpp)
REVERT: K  483 ARG cc_start: 0.6034 (ttm110) cc_final: 0.5464 (ptm160)
REVERT: K  496 GLU cc_start: 0.5480 (mm-30) cc_final: 0.4941 (tp30)
  outliers start: 12
  outliers final: 10
  residues processed: 131
  average time/residue: 0.1613
  time to fit residues: 28.4253
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  446 SER
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Chi-restraints excluded: chain K residue  499 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 114 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 134 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.150494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.111681 restraints weight = 22089.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 1.38
r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15865  Z= 0.150
  Angle     :  0.548  11.627  22637  Z= 0.324
  Chirality :  0.035   0.136   2547
  Planarity :  0.004   0.065   1861
  Dihedral  : 28.791 175.279   4411
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.52 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.25), residues: 1107
  helix:  2.62 (0.20), residues: 665
  sheet:  0.61 (0.70), residues: 61
  loop : -1.19 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  42 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.010   0.001   PHE C  25 
 TRP   0.007   0.001   TRP K 431 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (15861)
  covalent geometry    : angle       0.54753 (22634)
  hydrogen bonds       : bond        0.05798 (  864)
  hydrogen bonds       : angle       2.75129 ( 2194)
  metal coordination   : bond        0.00316 (    4)
  metal coordination   : angle       1.77951 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.433 
Fit side-chains
REVERT: F   91 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8550 (ttmm)
REVERT: G   99 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8479 (mmmt)
REVERT: K  180 ARG cc_start: 0.4609 (tpm170) cc_final: 0.3961 (mtm180)
REVERT: K  431 TRP cc_start: 0.7353 (m-10) cc_final: 0.7047 (m-10)
REVERT: K  472 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7216 (ptpp)
REVERT: K  483 ARG cc_start: 0.6044 (ttm110) cc_final: 0.5434 (ptm160)
REVERT: K  496 GLU cc_start: 0.5332 (mm-30) cc_final: 0.4846 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1630
  time to fit residues: 28.7813
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  472 LYS
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   chunk 85 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.112958 restraints weight = 22158.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.34
r_work: 0.2946 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15865  Z= 0.163
  Angle     :  0.545  12.125  22637  Z= 0.320
  Chirality :  0.035   0.150   2547
  Planarity :  0.004   0.061   1861
  Dihedral  : 28.688 175.008   4411
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.52 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.25), residues: 1107
  helix:  2.72 (0.20), residues: 660
  sheet:  1.29 (0.71), residues: 55
  loop : -1.23 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  42 
 TYR   0.009   0.001   TYR H  83 
 PHE   0.012   0.002   PHE C  25 
 TRP   0.007   0.001   TRP K 431 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15861)
  covalent geometry    : angle       0.54466 (22634)
  hydrogen bonds       : bond        0.05494 (  864)
  hydrogen bonds       : angle       2.72864 ( 2194)
  metal coordination   : bond        0.00283 (    4)
  metal coordination   : angle       1.71179 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.446 
Fit side-chains
REVERT: D   31 ARG cc_start: 0.4540 (ttt180) cc_final: 0.4008 (ttp-110)
REVERT: F   91 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8516 (ttmm)
REVERT: G   99 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8470 (mmmt)
REVERT: K  180 ARG cc_start: 0.4553 (tpm170) cc_final: 0.3915 (mtm180)
REVERT: K  430 MET cc_start: 0.7234 (mmm) cc_final: 0.6924 (mmp)
REVERT: K  483 ARG cc_start: 0.5933 (ttm110) cc_final: 0.5422 (ptm160)
REVERT: K  496 GLU cc_start: 0.5456 (mm-30) cc_final: 0.4930 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 128
  average time/residue: 0.1655
  time to fit residues: 28.4237
Evaluate side-chains
  124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 118 optimal weight:    0.0370
   overall best weight:    0.7658

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.151362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.113967 restraints weight = 22119.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.26
r_work: 0.2911 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15865  Z= 0.146
  Angle     :  0.537  12.551  22637  Z= 0.316
  Chirality :  0.034   0.150   2547
  Planarity :  0.004   0.059   1861
  Dihedral  : 28.663 175.001   4411
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.42 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.25), residues: 1107
  helix:  2.78 (0.20), residues: 660
  sheet:  1.28 (0.72), residues: 55
  loop : -1.19 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  42 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.009   0.001   PHE C  25 
 TRP   0.028   0.002   TRP K 431 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (15861)
  covalent geometry    : angle       0.53634 (22634)
  hydrogen bonds       : bond        0.05178 (  864)
  hydrogen bonds       : angle       2.70565 ( 2194)
  metal coordination   : bond        0.00334 (    4)
  metal coordination   : angle       1.85170 (    3)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.323 
Fit side-chains
REVERT: D   31 ARG cc_start: 0.4494 (ttt180) cc_final: 0.3975 (ttp-110)
REVERT: F   91 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8522 (ttmm)
REVERT: G   99 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8475 (mmmt)
REVERT: K  180 ARG cc_start: 0.4532 (tpm170) cc_final: 0.3918 (mtm180)
REVERT: K  483 ARG cc_start: 0.5941 (ttm110) cc_final: 0.5412 (ptm160)
REVERT: K  496 GLU cc_start: 0.5350 (mm-30) cc_final: 0.4886 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1664
  time to fit residues: 28.3231
Evaluate side-chains
  123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain K residue  214 VAL
Chi-restraints excluded: chain K residue  312 LEU
Chi-restraints excluded: chain K residue  450 ASP
Chi-restraints excluded: chain K residue  457 LEU
Chi-restraints excluded: chain K residue  481 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 98 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 125 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113441 restraints weight = 22043.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.37
r_work: 0.2897 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  15865  Z= 0.167
  Angle     :  0.728  59.134  22637  Z= 0.440
  Chirality :  0.034   0.243   2547
  Planarity :  0.004   0.053   1861
  Dihedral  : 28.665 175.005   4411
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.42 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.25), residues: 1107
  helix:  2.76 (0.20), residues: 660
  sheet:  1.28 (0.72), residues: 55
  loop : -1.18 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.009   0.001   PHE C  25 
 TRP   0.024   0.002   TRP K 431 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15861)
  covalent geometry    : angle       0.72735 (22634)
  hydrogen bonds       : bond        0.05215 (  864)
  hydrogen bonds       : angle       2.71776 ( 2194)
  metal coordination   : bond        0.00322 (    4)
  metal coordination   : angle       1.85186 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3014.56 seconds
wall clock time: 52 minutes 8.93 seconds (3128.93 seconds total)