Starting phenix.real_space_refine
on Fri Jun 13 12:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uv9_26809/06_2025/7uv9_26809.cif"
  }
  resolution = 3.2
  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=   0.002
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
     Fe      1      7.16       5
     P     292      5.49       5
     S      33      5.16       5
     C    8766      2.51       5
     N    2815      2.21       5
     O    3435      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15342
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 815
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    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: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    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: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3014
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2972
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 3379
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 407, 3379
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 19, 'TRANS': 387}
          Chain breaks: 3
    Chain: "K"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {' FE': 1, 'OH0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.86, per 1000 atoms: 0.58
  Number of scatterers: 15342
  At special positions: 0
  Unit cell: (91, 158.34, 152.88, 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)
     Fe      1     26.01
     S      33     16.00
     P     292     15.00
     O    3435      8.00
     N    2815      7.00
     C    8766      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: 3.34
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 11 sheets defined
      62.4% alpha, 6.6% beta
      142 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 6.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 3.553A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.649A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.570A  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
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.044A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.755A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (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: 3.501A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 47
      removed outlier: 3.569A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.736A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.817A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.834A  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: 3.781A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.587A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.866A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.715A  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: 3.604A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.515A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.602A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.644A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.501A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.766A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 39 through 46
    Processing helix  chain 'K' and resid 58 through 62
    Processing helix  chain 'K' and resid 63 through 71
    Processing helix  chain 'K' and resid 94 through 103
    Processing helix  chain 'K' and resid 123 through 132
    Processing helix  chain 'K' and resid 133 through 137
    Processing helix  chain 'K' and resid 153 through 157
    Processing helix  chain 'K' and resid 160 through 167
      removed outlier: 3.721A  pdb=" N   ASP K 164 " --> pdb=" O   PRO K 160 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE K 165 " --> pdb=" O   SER K 161 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE K 166 " --> pdb=" O   THR K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 173
      removed outlier: 3.583A  pdb=" N   TRP K 173 " --> pdb=" O   VAL K 169 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 174 through 179
    Processing helix  chain 'K' and resid 187 through 191
    Processing helix  chain 'K' and resid 214 through 218
    Processing helix  chain 'K' and resid 237 through 251
      removed outlier: 3.539A  pdb=" N   GLY K 251 " --> pdb=" O   TRP K 247 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 257 through 262
      removed outlier: 3.789A  pdb=" N   ARG K 261 " --> pdb=" O   PHE K 257 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 304 through 318
    Processing helix  chain 'K' and resid 321 through 325
    Processing helix  chain 'K' and resid 328 through 346
    Processing helix  chain 'K' and resid 351 through 363
    Processing helix  chain 'K' and resid 454 through 470
    Processing helix  chain 'K' and resid 472 through 477
      removed outlier: 4.420A  pdb=" N   CYS K 477 " --> pdb=" O   LEU K 473 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 484 through 500
    Processing helix  chain 'K' and resid 503 through 508
      removed outlier: 3.835A  pdb=" N   LEU K 508 " --> pdb=" O   PRO K 504 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.157A  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
      removed outlier: 3.547A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    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: 7.460A  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: 6.992A  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: 6.910A  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
      removed outlier: 3.574A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.072A  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 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 55 through 56
      removed outlier: 6.388A  pdb=" N   THR K  55 " --> pdb=" O   ILE K  77 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU K 293 " --> pdb=" O   HIS K 225 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   CYS K 200 " --> pdb=" O   SER K 145 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER K 145 " --> pdb=" O   CYS K 200 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE K 144 " --> pdb=" O   ASP K 109 " (cutoff:3.500A)
      removed outlier: 8.743A  pdb=" N   ASP K 109 " --> pdb=" O   ILE K 144 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   LEU K 146 " --> pdb=" O   MET K 107 " (cutoff:3.500A)
      removed outlier: 11.009A  pdb=" N   MET K 107 " --> pdb=" O   LEU K 146 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LYS K 117 " --> pdb=" O   ASP K 112 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 208 through 212
      removed outlier: 4.058A  pdb=" N   PHE K 211 " --> pdb=" O   HIS K 284 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   HIS K 284 " --> pdb=" O   PHE K 211 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1494 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      364 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 6.75

  Time building geometry restraints manager: 4.02 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1794
        1.30 -     1.44: 5928
        1.44 -     1.58: 7861
        1.58 -     1.72: 589
        1.72 -     1.86: 57
  Bond restraints: 16229
  Sorted by residual:
  bond pdb=" C   LYS K  79 "
       pdb=" O   LYS K  79 "
    ideal  model  delta    sigma   weight residual
    1.236  1.158  0.078 1.26e-02 6.30e+03 3.86e+01
  bond pdb=" CA  SER K 161 "
       pdb=" C   SER K 161 "
    ideal  model  delta    sigma   weight residual
    1.524  1.456  0.068 1.32e-02 5.74e+03 2.64e+01
  bond pdb=" CA  LEU K 464 "
       pdb=" C   LEU K 464 "
    ideal  model  delta    sigma   weight residual
    1.524  1.588 -0.065 1.27e-02 6.20e+03 2.59e+01
  bond pdb=" C   ILE K 305 "
       pdb=" O   ILE K 305 "
    ideal  model  delta    sigma   weight residual
    1.242  1.199  0.043 8.60e-03 1.35e+04 2.51e+01
  bond pdb=" CA  TYR K  49 "
       pdb=" C   TYR K  49 "
    ideal  model  delta    sigma   weight residual
    1.526  1.480  0.046 9.70e-03 1.06e+04 2.27e+01
  ... (remaining 16224 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 21514
        1.63 -     3.26: 1362
        3.26 -     4.89: 231
        4.89 -     6.52: 53
        6.52 -     8.15: 15
  Bond angle restraints: 23175
  Sorted by residual:
  angle pdb=" N   THR K 237 "
        pdb=" CA  THR K 237 "
        pdb=" C   THR K 237 "
      ideal   model   delta    sigma   weight residual
     110.53  103.44    7.09 1.32e+00 5.74e-01 2.89e+01
  angle pdb=" N   GLY K 481 "
        pdb=" CA  GLY K 481 "
        pdb=" C   GLY K 481 "
      ideal   model   delta    sigma   weight residual
     114.67  120.35   -5.68 1.10e+00 8.26e-01 2.67e+01
  angle pdb=" N   ASP K 491 "
        pdb=" CA  ASP K 491 "
        pdb=" C   ASP K 491 "
      ideal   model   delta    sigma   weight residual
     111.36  116.61   -5.25 1.09e+00 8.42e-01 2.32e+01
  angle pdb=" N   LEU K 359 "
        pdb=" CA  LEU K 359 "
        pdb=" C   LEU K 359 "
      ideal   model   delta    sigma   weight residual
     111.33  117.03   -5.70 1.21e+00 6.83e-01 2.22e+01
  angle pdb=" N   ILE K 311 "
        pdb=" CA  ILE K 311 "
        pdb=" C   ILE K 311 "
      ideal   model   delta    sigma   weight residual
     110.42  114.71   -4.29 9.60e-01 1.09e+00 2.00e+01
  ... (remaining 23170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.26: 7495
       35.26 -    70.53: 1455
       70.53 -   105.79: 25
      105.79 -   141.05: 0
      141.05 -   176.32: 1
  Dihedral angle restraints: 8976
    sinusoidal: 5597
      harmonic: 3379
  Sorted by residual:
  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   43.68  176.32     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  THR K 218 "
           pdb=" C   THR K 218 "
           pdb=" N   SER K 219 "
           pdb=" CA  SER K 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" C   PHE K 215 "
           pdb=" N   PHE K 215 "
           pdb=" CA  PHE K 215 "
           pdb=" CB  PHE K 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.37    8.77     0      2.50e+00 1.60e-01 1.23e+01
  ... (remaining 8973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 2227
       0.066 -    0.132: 275
       0.132 -    0.199: 77
       0.199 -    0.265: 19
       0.265 -    0.331: 8
  Chirality restraints: 2606
  Sorted by residual:
  chirality pdb=" CA  PHE K 215 "
            pdb=" N   PHE K 215 "
            pdb=" C   PHE K 215 "
            pdb=" CB  PHE K 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  THR K 209 "
            pdb=" N   THR K 209 "
            pdb=" C   THR K 209 "
            pdb=" CB  THR K 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.83   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  TYR K 222 "
            pdb=" N   TYR K 222 "
            pdb=" C   TYR K 222 "
            pdb=" CB  TYR K 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 2603 not shown)

  Planarity restraints: 1927
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   OH0 K 701 "    0.034 2.00e-02 2.50e+03   1.18e-01 2.09e+02
        pdb=" O   OH0 K 701 "   -0.164 2.00e-02 2.50e+03
        pdb=" C5  OH0 K 701 "   -0.156 2.00e-02 2.50e+03
        pdb=" C6  OH0 K 701 "    0.045 2.00e-02 2.50e+03
        pdb=" C7  OH0 K 701 "    0.112 2.00e-02 2.50e+03
        pdb=" O3  OH0 K 701 "    0.129 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 221 "    0.055 2.00e-02 2.50e+03   2.67e-02 1.79e+01
        pdb=" CG  TRP K 221 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 221 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 221 "   -0.040 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 221 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 221 "    0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 221 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 221 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 221 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 221 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 247 "    0.049 2.00e-02 2.50e+03   2.65e-02 1.75e+01
        pdb=" CG  TRP K 247 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 247 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 247 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 247 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 247 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 247 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 247 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 247 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 247 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1924 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 6
        2.23 -     2.90: 5058
        2.90 -     3.56: 21208
        3.56 -     4.23: 39510
        4.23 -     4.90: 60663
  Nonbonded interactions: 126445
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU K  41 "
            pdb=" NE2 HIS K  45 "
     model   vdw
     1.561 3.120
  nonbonded pdb=" O   OH0 K 701 "
            pdb="FE    FE K 702 "
     model   vdw
     2.037 2.260
  nonbonded pdb=" OD1 ASP K 214 "
            pdb="FE    FE K 702 "
     model   vdw
     2.159 2.260
  nonbonded pdb=" O3  OH0 K 701 "
            pdb="FE    FE K 702 "
     model   vdw
     2.203 2.260
  nonbonded pdb=" NE2 HIS K 212 "
            pdb="FE    FE K 702 "
     model   vdw
     2.208 2.340
  ... (remaining 126440 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 43 through 134)
  selection = (chain 'E' and resid 43 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 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=0.58 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.570
  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:          0.560
  Check model and map are aligned:         0.130
  Set scattering table:                    0.140
  Process input model:                     39.070
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
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   0.093  16229  Z= 0.550
  Angle     :  0.890   8.149  23175  Z= 0.554
  Chirality :  0.055   0.331   2606
  Planarity :  0.007   0.118   1927
  Dihedral  : 26.048 176.319   6798
  Min Nonbonded Distance : 1.561

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.41 %
    Favored  : 97.29 %
  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:  1.22 (0.25), residues: 1138
  helix:  1.94 (0.21), residues: 645
  sheet:  0.84 (0.64), residues: 63
  loop : -0.99 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.015   TRP K 247 
 HIS   0.021   0.004   HIS K 225 
 PHE   0.058   0.007   PHE K 215 
 TYR   0.042   0.005   TYR K 222 
 ARG   0.029   0.001   ARG K 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11749 (  886)
  hydrogen bonds       : angle       4.01512 ( 2222)
  covalent geometry    : bond        0.00861 (16229)
  covalent geometry    : angle       0.88987 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7756 (t0) cc_final: 0.7396 (t0)
REVERT: D   31 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3048 (ttm110)
REVERT: K  120 GLU cc_start: 0.4573 (mt-10) cc_final: 0.4120 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 168
  average time/residue: 0.3500
  time to fit residues: 80.7064
Evaluate side-chains
  139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   31 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  24 GLN
C  73 ASN
C 104 GLN
F  25 ASN
K 176 HIS
K 226 GLN
** K 308 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 = 0.4214 r_free = 0.4214 target = 0.172923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.134664 restraints weight = 26235.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 3.03
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  16229  Z= 0.260
  Angle     :  0.665   5.784  23175  Z= 0.391
  Chirality :  0.042   0.159   2606
  Planarity :  0.006   0.047   1927
  Dihedral  : 29.524 179.283   4485
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.32 %
    Favored  : 91.57 %
  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:  1.06 (0.25), residues: 1138
  helix:  1.65 (0.20), residues: 675
  sheet:  0.88 (0.64), residues: 66
  loop : -1.01 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP K 247 
 HIS   0.007   0.001   HIS K 223 
 PHE   0.023   0.003   PHE K  93 
 TYR   0.015   0.002   TYR K 330 
 ARG   0.006   0.001   ARG K 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08718 (  886)
  hydrogen bonds       : angle       3.57865 ( 2222)
  covalent geometry    : bond        0.00591 (16229)
  covalent geometry    : angle       0.66533 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7955 (t0) cc_final: 0.7480 (t0)
REVERT: K  191 MET cc_start: 0.1364 (mtt) cc_final: 0.0649 (tpt)
REVERT: K  332 MET cc_start: 0.1921 (tpp) cc_final: 0.0929 (tpp)
REVERT: K  466 ASP cc_start: 0.1145 (OUTLIER) cc_final: 0.0905 (p0)
  outliers start: 11
  outliers final: 4
  residues processed: 151
  average time/residue: 0.3742
  time to fit residues: 77.2812
Evaluate side-chains
  133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  201 LEU
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 113 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 132 optimal weight:    0.5980
   chunk 121 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 124 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0170
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
H  49 HIS
H 109 HIS
K 114 ASN
** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 515 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.176708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.135840 restraints weight = 26431.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.89
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16229  Z= 0.144
  Angle     :  0.535   8.799  23175  Z= 0.320
  Chirality :  0.035   0.141   2606
  Planarity :  0.004   0.048   1927
  Dihedral  : 29.274 177.725   4481
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  9.23 %
    Favored  : 90.17 %
  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:  1.76 (0.25), residues: 1138
  helix:  2.26 (0.20), residues: 667
  sheet:  1.12 (0.64), residues: 66
  loop : -0.72 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K 247 
 HIS   0.003   0.001   HIS K 150 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.016   0.001   TYR K 222 
 ARG   0.003   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05282 (  886)
  hydrogen bonds       : angle       3.17167 ( 2222)
  covalent geometry    : bond        0.00297 (16229)
  covalent geometry    : angle       0.53509 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7896 (t0) cc_final: 0.7341 (t0)
REVERT: D   52 THR cc_start: 0.8258 (m) cc_final: 0.7954 (m)
REVERT: K  191 MET cc_start: 0.1426 (mtt) cc_final: 0.0085 (tpt)
REVERT: K  466 ASP cc_start: 0.1015 (OUTLIER) cc_final: 0.0809 (p0)
  outliers start: 6
  outliers final: 3
  residues processed: 141
  average time/residue: 0.4182
  time to fit residues: 79.9051
Evaluate side-chains
  129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 129 optimal weight:   10.0000
   chunk 61 optimal weight:    0.6980
   chunk 98 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
K 308 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.174669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136318 restraints weight = 26112.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.82
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16229  Z= 0.172
  Angle     :  0.562  10.662  23175  Z= 0.333
  Chirality :  0.037   0.153   2606
  Planarity :  0.004   0.045   1927
  Dihedral  : 29.312 178.783   4481
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.43 %
    Favored  : 88.26 %
  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:  1.53 (0.25), residues: 1138
  helix:  2.14 (0.20), residues: 672
  sheet:  1.12 (0.63), residues: 66
  loop : -1.00 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K 221 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.010   0.001   PHE K 215 
 TYR   0.021   0.001   TYR K 222 
 ARG   0.006   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06414 (  886)
  hydrogen bonds       : angle       3.17290 ( 2222)
  covalent geometry    : bond        0.00373 (16229)
  covalent geometry    : angle       0.56153 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7915 (t0) cc_final: 0.7378 (t0)
REVERT: D   52 THR cc_start: 0.8235 (m) cc_final: 0.7954 (m)
REVERT: K  191 MET cc_start: 0.1458 (mtt) cc_final: 0.0147 (tpt)
REVERT: K  332 MET cc_start: 0.1730 (tpp) cc_final: 0.0782 (tpp)
  outliers start: 13
  outliers final: 9
  residues processed: 139
  average time/residue: 0.5215
  time to fit residues: 99.3309
Evaluate side-chains
  133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 18 optimal weight:    0.0980
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0060
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.177007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136473 restraints weight = 26680.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.39
r_work: 0.3138 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16229  Z= 0.138
  Angle     :  0.519   9.636  23175  Z= 0.310
  Chirality :  0.035   0.131   2606
  Planarity :  0.004   0.045   1927
  Dihedral  : 29.179 178.318   4481
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.63 %
    Favored  : 87.36 %
  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:  1.99 (0.25), residues: 1138
  helix:  2.47 (0.20), residues: 670
  sheet:  1.45 (0.63), residues: 64
  loop : -0.75 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 126 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE K 215 
 TYR   0.015   0.001   TYR K 130 
 ARG   0.005   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04922 (  886)
  hydrogen bonds       : angle       2.99020 ( 2222)
  covalent geometry    : bond        0.00285 (16229)
  covalent geometry    : angle       0.51888 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8081 (t0) cc_final: 0.7449 (t0)
REVERT: D   52 THR cc_start: 0.8395 (m) cc_final: 0.8078 (m)
REVERT: K  172 MET cc_start: 0.0330 (mpp) cc_final: -0.0235 (mmp)
REVERT: K  191 MET cc_start: -0.0009 (mtt) cc_final: -0.0263 (tpt)
REVERT: K  199 TYR cc_start: 0.3978 (OUTLIER) cc_final: 0.3369 (t80)
REVERT: K  202 MET cc_start: 0.2288 (mtm) cc_final: 0.1721 (tpt)
REVERT: K  332 MET cc_start: 0.0081 (tpp) cc_final: -0.0152 (mmt)
  outliers start: 10
  outliers final: 7
  residues processed: 137
  average time/residue: 0.3621
  time to fit residues: 67.6835
Evaluate side-chains
  134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 126 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 137 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.173977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135793 restraints weight = 26385.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.94
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16229  Z= 0.189
  Angle     :  0.573   9.112  23175  Z= 0.339
  Chirality :  0.037   0.133   2606
  Planarity :  0.004   0.043   1927
  Dihedral  : 29.323 179.740   4481
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.54 %
    Favored  : 86.16 %
  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:  1.56 (0.25), residues: 1138
  helix:  2.17 (0.20), residues: 672
  sheet:  1.22 (0.62), residues: 66
  loop : -1.04 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K 221 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.001   PHE K 215 
 TYR   0.013   0.001   TYR K 330 
 ARG   0.006   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06914 (  886)
  hydrogen bonds       : angle       3.16319 ( 2222)
  covalent geometry    : bond        0.00416 (16229)
  covalent geometry    : angle       0.57279 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7961 (t0) cc_final: 0.7391 (t0)
REVERT: D   52 THR cc_start: 0.8257 (m) cc_final: 0.7969 (m)
REVERT: K  191 MET cc_start: 0.1494 (mtt) cc_final: 0.0375 (tpt)
REVERT: K  332 MET cc_start: 0.1689 (tpp) cc_final: 0.0809 (tpp)
  outliers start: 13
  outliers final: 11
  residues processed: 132
  average time/residue: 0.3998
  time to fit residues: 72.5187
Evaluate side-chains
  129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 124 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D 109 HIS
K 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.172302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.133989 restraints weight = 26287.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 3.39
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  16229  Z= 0.236
  Angle     :  0.637   9.125  23175  Z= 0.372
  Chirality :  0.040   0.142   2606
  Planarity :  0.005   0.042   1927
  Dihedral  : 29.521 179.070   4481
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.64 %
    Favored  : 85.96 %
  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:  1.19 (0.25), residues: 1138
  helix:  1.90 (0.20), residues: 673
  sheet:  0.77 (0.60), residues: 66
  loop : -1.20 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 516 
 HIS   0.006   0.001   HIS G  31 
 PHE   0.015   0.002   PHE K 257 
 TYR   0.018   0.002   TYR K 330 
 ARG   0.006   0.001   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08033 (  886)
  hydrogen bonds       : angle       3.36614 ( 2222)
  covalent geometry    : bond        0.00533 (16229)
  covalent geometry    : angle       0.63728 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8033 (t0) cc_final: 0.7525 (t0)
REVERT: K   14 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6121 (tt)
REVERT: K   93 PHE cc_start: 0.1966 (OUTLIER) cc_final: 0.0799 (m-80)
REVERT: K  191 MET cc_start: 0.1377 (mtt) cc_final: 0.0538 (tpt)
REVERT: K  202 MET cc_start: 0.3713 (mmt) cc_final: 0.2766 (mtp)
REVERT: K  332 MET cc_start: 0.1722 (tpp) cc_final: 0.0938 (mmt)
  outliers start: 14
  outliers final: 11
  residues processed: 134
  average time/residue: 0.3624
  time to fit residues: 66.5098
Evaluate side-chains
  130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue   93 PHE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 106 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.174196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132713 restraints weight = 26185.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.94
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
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   0.037  16229  Z= 0.174
  Angle     :  0.572   8.677  23175  Z= 0.338
  Chirality :  0.037   0.134   2606
  Planarity :  0.004   0.043   1927
  Dihedral  : 29.377 179.120   4481
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.14 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.47 (0.25), residues: 1138
  helix:  2.16 (0.20), residues: 668
  sheet:  0.52 (0.61), residues: 68
  loop : -1.05 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP K 334 
 HIS   0.004   0.001   HIS K 176 
 PHE   0.011   0.001   PHE K 257 
 TYR   0.011   0.001   TYR K 222 
 ARG   0.005   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06358 (  886)
  hydrogen bonds       : angle       3.17398 ( 2222)
  covalent geometry    : bond        0.00379 (16229)
  covalent geometry    : angle       0.57183 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.372 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.8025 (t0) cc_final: 0.7490 (t0)
REVERT: D   52 THR cc_start: 0.8314 (m) cc_final: 0.8008 (m)
REVERT: K   14 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6037 (tt)
REVERT: K  191 MET cc_start: 0.1541 (mtt) cc_final: 0.0701 (tpt)
REVERT: K  202 MET cc_start: 0.3590 (mmt) cc_final: 0.2825 (mtp)
REVERT: K  332 MET cc_start: 0.2010 (tpp) cc_final: 0.1107 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 133
  average time/residue: 0.3722
  time to fit residues: 67.5397
Evaluate side-chains
  133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 132 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.175392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.134438 restraints weight = 26191.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.86
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16229  Z= 0.153
  Angle     :  0.559  11.443  23175  Z= 0.327
  Chirality :  0.036   0.133   2606
  Planarity :  0.004   0.044   1927
  Dihedral  : 29.286 178.888   4481
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.54 %
    Favored  : 85.36 %
  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:  1.70 (0.25), residues: 1138
  helix:  2.35 (0.20), residues: 669
  sheet:  0.81 (0.62), residues: 64
  loop : -0.98 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP K 334 
 HIS   0.005   0.001   HIS K 176 
 PHE   0.019   0.001   PHE K 324 
 TYR   0.023   0.001   TYR K 199 
 ARG   0.006   0.000   ARG K 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05569 (  886)
  hydrogen bonds       : angle       3.08309 ( 2222)
  covalent geometry    : bond        0.00326 (16229)
  covalent geometry    : angle       0.55863 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 1.245 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7952 (t0) cc_final: 0.7418 (t0)
REVERT: D   52 THR cc_start: 0.8265 (m) cc_final: 0.7937 (m)
REVERT: K   14 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5912 (tt)
REVERT: K  191 MET cc_start: 0.1624 (mtt) cc_final: 0.0912 (tpt)
REVERT: K  202 MET cc_start: 0.3236 (mmt) cc_final: 0.2820 (mtp)
REVERT: K  222 TYR cc_start: 0.3651 (t80) cc_final: 0.3283 (m-80)
REVERT: K  317 ARG cc_start: 0.4155 (mtp-110) cc_final: 0.2962 (ptm-80)
REVERT: K  332 MET cc_start: 0.2291 (tpp) cc_final: 0.1230 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 134
  average time/residue: 0.3793
  time to fit residues: 68.8302
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  300 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 129 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
K 158 GLN
K 197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.172167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.130152 restraints weight = 26086.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.25
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  16229  Z= 0.251
  Angle     :  0.655   8.699  23175  Z= 0.379
  Chirality :  0.041   0.140   2606
  Planarity :  0.005   0.042   1927
  Dihedral  : 29.501 179.329   4481
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.74 %
    Favored  : 85.06 %
  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:  1.16 (0.25), residues: 1138
  helix:  1.91 (0.20), residues: 674
  sheet:  0.40 (0.62), residues: 68
  loop : -1.20 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP K 334 
 HIS   0.007   0.001   HIS G  31 
 PHE   0.016   0.002   PHE K 257 
 TYR   0.020   0.002   TYR K 330 
 ARG   0.006   0.001   ARG K 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08123 (  886)
  hydrogen bonds       : angle       3.39533 ( 2222)
  covalent geometry    : bond        0.00572 (16229)
  covalent geometry    : angle       0.65518 (23175)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.170 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.8023 (t0) cc_final: 0.7523 (t0)
REVERT: K   14 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6105 (tt)
REVERT: K  191 MET cc_start: 0.1541 (mtt) cc_final: 0.0820 (tpt)
REVERT: K  202 MET cc_start: 0.3868 (mmt) cc_final: 0.2930 (mtp)
REVERT: K  332 MET cc_start: 0.2112 (tpp) cc_final: 0.1212 (mmt)
REVERT: K  469 GLU cc_start: 0.4225 (mm-30) cc_final: 0.3790 (mm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 132
  average time/residue: 0.3618
  time to fit residues: 64.8169
Evaluate side-chains
  128 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   77 ILE
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 117 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 135 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.173276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134644 restraints weight = 26048.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.95
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16229  Z= 0.194
  Angle     :  0.598   8.553  23175  Z= 0.350
  Chirality :  0.038   0.138   2606
  Planarity :  0.004   0.045   1927
  Dihedral  : 29.416 179.804   4481
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.54 %
    Favored  : 85.46 %
  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:  1.32 (0.25), residues: 1138
  helix:  2.06 (0.20), residues: 675
  sheet:  0.65 (0.63), residues: 64
  loop : -1.21 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP K 334 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.012   0.002   PHE K 257 
 TYR   0.016   0.002   TYR K 130 
 ARG   0.007   0.000   ARG K 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06853 (  886)
  hydrogen bonds       : angle       3.26896 ( 2222)
  covalent geometry    : bond        0.00431 (16229)
  covalent geometry    : angle       0.59831 (23175)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6327.39 seconds
wall clock time: 112 minutes 23.29 seconds (6743.29 seconds total)