Starting phenix.real_space_refine
on Tue Apr 29 18:15:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yn2_39412/04_2025/8yn2_39412.cif"
  }
  resolution = 2.66
  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=   0.013
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5763      2.51       5
     N    1531      2.21       5
     O    1625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8979
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1798
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 50
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2196
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 262}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "R"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 148
          Unusual residues: {'CLR': 5, 'HSM': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 5.77, per 1000 atoms: 0.64
  Number of scatterers: 8979
  At special positions: 0
  Unit cell: (97.37, 107, 117.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1625      8.00
     N    1531      7.00
     C    5763      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 441 " - pdb=" SG  CYS R 444 " distance=2.03

  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: 2.38
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      40.7% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.557A  pdb=" N   ARG A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.663A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 4.152A  pdb=" N   ARG A 135 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.318A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 3.586A  pdb=" N   PHE A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 356
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.509A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.526A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 55
      removed outlier: 3.570A  pdb=" N   ARG R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 79
      removed outlier: 4.188A  pdb=" N   TYR R  65 " --> pdb=" O   VAL R  61 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE R  66 " --> pdb=" O   GLY R  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 90
      removed outlier: 3.562A  pdb=" N   MET R  83 " --> pdb=" O   VAL R  79 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 131
    Processing helix  chain 'R' and resid 131 through 138
      removed outlier: 3.544A  pdb=" N   LEU R 136 " --> pdb=" O   PRO R 132 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LYS R 137 " --> pdb=" O   LEU R 133 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   TYR R 138 " --> pdb=" O   ARG R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 156
    Processing helix  chain 'R' and resid 158 through 164
    Processing helix  chain 'R' and resid 164 through 169
    Processing helix  chain 'R' and resid 182 through 186
      removed outlier: 4.446A  pdb=" N   ASP R 186 " --> pdb=" O   ASP R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 3.863A  pdb=" N   LYS R 191 " --> pdb=" O   VAL R 187 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 225
    Processing helix  chain 'R' and resid 410 through 442
      removed outlier: 3.542A  pdb=" N   PHE R 424 " --> pdb=" O   ILE R 420 " (cutoff:3.500A)
      Proline residue:  R 430  - end of helix
      removed outlier: 3.681A  pdb=" N   MET R 436 " --> pdb=" O   PHE R 432 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ALA R 439 " --> pdb=" O   PHE R 435 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 446 through 472
      removed outlier: 3.805A  pdb=" N   SER R 461 " --> pdb=" O   GLY R 457 " (cutoff:3.500A)
      Proline residue:  R 465  - end of helix
      Proline residue:  R 469  - end of helix
      removed outlier: 3.731A  pdb=" N   ASN R 472 " --> pdb=" O   TYR R 468 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 472 through 485
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76
      removed outlier: 6.177A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.804A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.626A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.751A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.963A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.296A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.384A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.514A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.738A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.794A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.305A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.106A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1299 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2869
        1.34 -     1.46: 2246
        1.46 -     1.58: 3985
        1.58 -     1.70: 0
        1.70 -     1.82: 87
  Bond restraints: 9187
  Sorted by residual:
  bond pdb=" CG  HSM R 701 "
       pdb=" ND1 HSM R 701 "
    ideal  model  delta    sigma   weight residual
    1.383  1.338  0.045 2.00e-02 2.50e+03 5.03e+00
  bond pdb=" C5  CLR R 706 "
       pdb=" C6  CLR R 706 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" C5  CLR R 703 "
       pdb=" C6  CLR R 703 "
    ideal  model  delta    sigma   weight residual
    1.332  1.299  0.033 2.00e-02 2.50e+03 2.80e+00
  bond pdb=" C5  CLR R 704 "
       pdb=" C6  CLR R 704 "
    ideal  model  delta    sigma   weight residual
    1.332  1.299  0.033 2.00e-02 2.50e+03 2.74e+00
  bond pdb=" C5  CLR R 705 "
       pdb=" C6  CLR R 705 "
    ideal  model  delta    sigma   weight residual
    1.332  1.299  0.033 2.00e-02 2.50e+03 2.72e+00
  ... (remaining 9182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12249
        1.64 -     3.29: 174
        3.29 -     4.93: 38
        4.93 -     6.57: 21
        6.57 -     8.21: 4
  Bond angle restraints: 12486
  Sorted by residual:
  angle pdb=" C13 CLR R 704 "
        pdb=" C17 CLR R 704 "
        pdb=" C20 CLR R 704 "
      ideal   model   delta    sigma   weight residual
     119.60  111.39    8.21 3.00e+00 1.11e-01 7.50e+00
  angle pdb=" C13 CLR R 702 "
        pdb=" C17 CLR R 702 "
        pdb=" C20 CLR R 702 "
      ideal   model   delta    sigma   weight residual
     119.60  111.42    8.18 3.00e+00 1.11e-01 7.44e+00
  angle pdb=" C13 CLR R 705 "
        pdb=" C17 CLR R 705 "
        pdb=" C20 CLR R 705 "
      ideal   model   delta    sigma   weight residual
     119.60  111.60    8.00 3.00e+00 1.11e-01 7.12e+00
  angle pdb=" C13 CLR R 703 "
        pdb=" C17 CLR R 703 "
        pdb=" C20 CLR R 703 "
      ideal   model   delta    sigma   weight residual
     119.60  111.75    7.85 3.00e+00 1.11e-01 6.84e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.94   -4.40 1.91e+00 2.74e-01 5.30e+00
  ... (remaining 12481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 5346
       15.12 -    30.24: 241
       30.24 -    45.36: 65
       45.36 -    60.48: 17
       60.48 -    75.60: 2
  Dihedral angle restraints: 5671
    sinusoidal: 2384
      harmonic: 3287
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.20   18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.74   18.26     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5668 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1329
       0.099 -    0.198: 75
       0.198 -    0.297: 5
       0.297 -    0.395: 5
       0.395 -    0.494: 5
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" C14 CLR R 704 "
            pdb=" C13 CLR R 704 "
            pdb=" C15 CLR R 704 "
            pdb=" C8  CLR R 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.81    0.49 2.00e-01 2.50e+01 6.11e+00
  chirality pdb=" C14 CLR R 702 "
            pdb=" C13 CLR R 702 "
            pdb=" C15 CLR R 702 "
            pdb=" C8  CLR R 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.80    0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" C14 CLR R 705 "
            pdb=" C13 CLR R 705 "
            pdb=" C15 CLR R 705 "
            pdb=" C8  CLR R 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.79    0.47 2.00e-01 2.50e+01 5.55e+00
  ... (remaining 1416 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO B 236 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO B 194 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 184 "   -0.016 5.00e-02 4.00e+02   2.47e-02 9.79e-01
        pdb=" N   PRO E 185 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO E 185 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 185 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 317
        2.72 -     3.27: 8894
        3.27 -     3.81: 14811
        3.81 -     4.36: 19092
        4.36 -     4.90: 32503
  Nonbonded interactions: 75617
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OG1 THR R  41 "
            pdb=" OG1 THR R 462 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   THR R  41 "
            pdb=" ND2 ASN R  45 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   LYS C  20 "
            pdb=" ND2 ASN C  24 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" NE2 GLN A  52 "
            pdb=" O   ALA A 218 "
     model   vdw
     2.303 3.120
  ... (remaining 75612 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.640
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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      :  0.003   0.045   9191  Z= 0.136
  Angle     :  0.559   8.214  12494  Z= 0.251
  Chirality :  0.058   0.494   1419
  Planarity :  0.003   0.043   1551
  Dihedral  :  9.777  75.596   3537
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  2.97 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.29 (0.25), residues: 1113
  helix:  1.30 (0.25), residues: 401
  sheet:  0.81 (0.30), residues: 285
  loop :  0.66 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.002   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23616 (  461)
  hydrogen bonds       : angle       7.08438 ( 1299)
  SS BOND              : bond        0.00086 (    4)
  SS BOND              : angle       0.70343 (    8)
  covalent geometry    : bond        0.00302 ( 9187)
  covalent geometry    : angle       0.55897 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 210
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8554 (mttt) cc_final: 0.8242 (mtmt)
REVERT: A   21 LYS cc_start: 0.8540 (tttm) cc_final: 0.8055 (mtmm)
REVERT: A   73 LYS cc_start: 0.8531 (mttt) cc_final: 0.8315 (mptt)
REVERT: A  208 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7274 (mtm180)
REVERT: A  346 ASP cc_start: 0.8003 (m-30) cc_final: 0.7570 (t0)
REVERT: B   16 ASN cc_start: 0.7831 (m-40) cc_final: 0.7597 (m110)
REVERT: B  130 GLU cc_start: 0.8422 (mp0) cc_final: 0.8185 (mp0)
REVERT: B  134 ARG cc_start: 0.8369 (ptt180) cc_final: 0.8115 (ptp90)
REVERT: B  135 VAL cc_start: 0.9322 (t) cc_final: 0.9080 (p)
REVERT: B  186 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (m-30)
REVERT: B  188 MET cc_start: 0.8971 (mmm) cc_final: 0.8685 (mmm)
REVERT: C   20 LYS cc_start: 0.8683 (mttt) cc_final: 0.8346 (mttm)
REVERT: E   43 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7648 (mtpt)
REVERT: R   55 GLU cc_start: 0.7388 (tp30) cc_final: 0.6897 (tp30)
REVERT: R   57 LYS cc_start: 0.8056 (mttt) cc_final: 0.7438 (pttp)
REVERT: R  176 ARG cc_start: 0.7487 (ptp90) cc_final: 0.7186 (ptp90)
REVERT: R  179 LYS cc_start: 0.7501 (mmtt) cc_final: 0.6869 (mmmm)
REVERT: R  215 LYS cc_start: 0.7502 (tppt) cc_final: 0.7287 (mppt)
REVERT: R  218 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7736 (ttp-170)
REVERT: R  470 LEU cc_start: 0.7968 (tt) cc_final: 0.7440 (mm)
  outliers start: 6
  outliers final: 3
  residues processed: 213
  average time/residue: 1.4259
  time to fit residues: 321.5011
Evaluate side-chains
  156 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  441 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    0.1980
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 116 ASN
A 350 GLN
B  91 HIS
B 176 GLN
B 220 GLN
R 166 ASN
R 472 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.109728 restraints weight = 10841.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 1.97
r_work: 0.3111 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9191  Z= 0.123
  Angle     :  0.527   6.090  12494  Z= 0.283
  Chirality :  0.043   0.183   1419
  Planarity :  0.004   0.043   1551
  Dihedral  :  6.115  57.068   1568
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.77 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.90 (0.25), residues: 1113
  helix:  2.41 (0.25), residues: 394
  sheet:  1.00 (0.30), residues: 270
  loop :  0.48 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.014   0.001   PHE A  74 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.008   0.001   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  461)
  hydrogen bonds       : angle       4.86312 ( 1299)
  SS BOND              : bond        0.00323 (    4)
  SS BOND              : angle       1.07357 (    8)
  covalent geometry    : bond        0.00257 ( 9187)
  covalent geometry    : angle       0.52602 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8516 (mttt) cc_final: 0.8142 (mtmt)
REVERT: A   82 HIS cc_start: 0.8232 (t-90) cc_final: 0.7871 (t-170)
REVERT: A  208 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7330 (mtm180)
REVERT: B  130 GLU cc_start: 0.8469 (mp0) cc_final: 0.8001 (mp0)
REVERT: B  134 ARG cc_start: 0.8647 (ptt180) cc_final: 0.8398 (ptt-90)
REVERT: B  188 MET cc_start: 0.8947 (mmm) cc_final: 0.8579 (mmm)
REVERT: E   43 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7692 (mtpt)
REVERT: E  213 THR cc_start: 0.8620 (p) cc_final: 0.8157 (t)
REVERT: R   55 GLU cc_start: 0.7154 (tp30) cc_final: 0.6946 (tp30)
REVERT: R   57 LYS cc_start: 0.8035 (mttt) cc_final: 0.7616 (mtmm)
REVERT: R  470 LEU cc_start: 0.7902 (tt) cc_final: 0.7476 (mm)
  outliers start: 19
  outliers final: 7
  residues processed: 161
  average time/residue: 1.2383
  time to fit residues: 212.7385
Evaluate side-chains
  153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0170
   chunk 37 optimal weight:    0.5980
   chunk 94 optimal weight:    0.3980
   chunk 50 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  13 GLN
B  16 ASN
E 171 ASN
E 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.145111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.103204 restraints weight = 10461.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.11
r_work: 0.3009 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9191  Z= 0.106
  Angle     :  0.485   5.859  12494  Z= 0.258
  Chirality :  0.041   0.141   1419
  Planarity :  0.004   0.043   1551
  Dihedral  :  5.770  55.981   1564
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.31 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.10 (0.25), residues: 1113
  helix:  2.84 (0.25), residues: 391
  sheet:  0.88 (0.30), residues: 270
  loop :  0.51 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.018   0.001   PHE R 434 
 TYR   0.017   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  461)
  hydrogen bonds       : angle       4.56886 ( 1299)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       0.87355 (    8)
  covalent geometry    : bond        0.00219 ( 9187)
  covalent geometry    : angle       0.48489 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8335 (mttt) cc_final: 0.7947 (mtmt)
REVERT: A   82 HIS cc_start: 0.8126 (t-90) cc_final: 0.7716 (t-170)
REVERT: A  208 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7260 (mtm180)
REVERT: B  130 GLU cc_start: 0.8441 (mp0) cc_final: 0.7962 (mp0)
REVERT: B  134 ARG cc_start: 0.8644 (ptt180) cc_final: 0.8387 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8798 (t70) cc_final: 0.8537 (t0)
REVERT: E   43 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7482 (mtpt)
REVERT: E  213 THR cc_start: 0.8565 (p) cc_final: 0.8096 (t)
REVERT: R   57 LYS cc_start: 0.7893 (mttt) cc_final: 0.7459 (mtmm)
REVERT: R  470 LEU cc_start: 0.7807 (tt) cc_final: 0.7304 (mm)
  outliers start: 23
  outliers final: 10
  residues processed: 163
  average time/residue: 1.2748
  time to fit residues: 221.8239
Evaluate side-chains
  146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 90 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN
R 198 ASN
R 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.145539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107424 restraints weight = 10881.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.00
r_work: 0.3065 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9191  Z= 0.145
  Angle     :  0.514   6.129  12494  Z= 0.272
  Chirality :  0.042   0.141   1419
  Planarity :  0.004   0.044   1551
  Dihedral  :  5.805  55.175   1564
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.23 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.03 (0.25), residues: 1113
  helix:  2.89 (0.25), residues: 390
  sheet:  0.72 (0.31), residues: 266
  loop :  0.45 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.014   0.001   PHE R 435 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.008   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  461)
  hydrogen bonds       : angle       4.57241 ( 1299)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.98395 (    8)
  covalent geometry    : bond        0.00329 ( 9187)
  covalent geometry    : angle       0.51352 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8471 (mttt) cc_final: 0.8103 (mtmt)
REVERT: A   82 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7739 (t-170)
REVERT: A  208 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7375 (mtm180)
REVERT: A  217 CYS cc_start: 0.8213 (m) cc_final: 0.7908 (t)
REVERT: B  130 GLU cc_start: 0.8505 (mp0) cc_final: 0.8115 (mp0)
REVERT: B  134 ARG cc_start: 0.8715 (ptt180) cc_final: 0.8456 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8858 (t70) cc_final: 0.8641 (t0)
REVERT: E   43 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7929 (mmpt)
REVERT: E  213 THR cc_start: 0.8681 (p) cc_final: 0.8245 (t)
REVERT: R   55 GLU cc_start: 0.7209 (tp30) cc_final: 0.6947 (tp30)
REVERT: R   57 LYS cc_start: 0.8051 (mttt) cc_final: 0.7440 (pttp)
REVERT: R  470 LEU cc_start: 0.7973 (tt) cc_final: 0.7468 (mm)
  outliers start: 24
  outliers final: 13
  residues processed: 155
  average time/residue: 1.3796
  time to fit residues: 228.0891
Evaluate side-chains
  150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 28 optimal weight:    0.3980
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0020
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN
R 472 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.147306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.109484 restraints weight = 10886.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.02
r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9191  Z= 0.105
  Angle     :  0.487   9.513  12494  Z= 0.254
  Chirality :  0.041   0.143   1419
  Planarity :  0.003   0.042   1551
  Dihedral  :  5.599  55.589   1564
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.44 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.11 (0.26), residues: 1113
  helix:  3.06 (0.25), residues: 390
  sheet:  0.68 (0.31), residues: 268
  loop :  0.45 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.013   0.001   PHE R 434 
 TYR   0.018   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  461)
  hydrogen bonds       : angle       4.40885 ( 1299)
  SS BOND              : bond        0.00276 (    4)
  SS BOND              : angle       0.82747 (    8)
  covalent geometry    : bond        0.00226 ( 9187)
  covalent geometry    : angle       0.48694 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8428 (mttt) cc_final: 0.8047 (mtmt)
REVERT: A   82 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7784 (t-170)
REVERT: A  208 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7378 (mtm180)
REVERT: A  217 CYS cc_start: 0.8336 (m) cc_final: 0.8034 (t)
REVERT: B  130 GLU cc_start: 0.8523 (mp0) cc_final: 0.8090 (mp0)
REVERT: B  134 ARG cc_start: 0.8691 (ptt180) cc_final: 0.8421 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8816 (t70) cc_final: 0.8562 (t0)
REVERT: B  327 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8843 (p)
REVERT: E   43 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7692 (mtpt)
REVERT: E  213 THR cc_start: 0.8667 (p) cc_final: 0.8240 (t)
REVERT: E  217 SER cc_start: 0.8352 (m) cc_final: 0.7964 (p)
REVERT: R   57 LYS cc_start: 0.7934 (mttt) cc_final: 0.7335 (pttp)
REVERT: R  470 LEU cc_start: 0.7943 (tt) cc_final: 0.7469 (mm)
  outliers start: 24
  outliers final: 14
  residues processed: 158
  average time/residue: 1.1954
  time to fit residues: 201.8323
Evaluate side-chains
  148 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN
R  84 ASN
R 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.109368 restraints weight = 10779.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.01
r_work: 0.3117 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9191  Z= 0.109
  Angle     :  0.491   8.634  12494  Z= 0.256
  Chirality :  0.041   0.134   1419
  Planarity :  0.003   0.041   1551
  Dihedral  :  5.547  55.851   1564
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.39 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.12 (0.26), residues: 1113
  helix:  3.09 (0.25), residues: 391
  sheet:  0.63 (0.30), residues: 268
  loop :  0.48 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.011   0.001   PHE A  74 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  461)
  hydrogen bonds       : angle       4.34394 ( 1299)
  SS BOND              : bond        0.00292 (    4)
  SS BOND              : angle       0.85235 (    8)
  covalent geometry    : bond        0.00237 ( 9187)
  covalent geometry    : angle       0.49055 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8440 (mttt) cc_final: 0.8055 (mtmt)
REVERT: A   31 ARG cc_start: 0.8299 (mtt90) cc_final: 0.8071 (mtt90)
REVERT: A   82 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (t-170)
REVERT: A  208 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7390 (mtm180)
REVERT: A  217 CYS cc_start: 0.8325 (m) cc_final: 0.8024 (t)
REVERT: B  130 GLU cc_start: 0.8504 (mp0) cc_final: 0.8058 (mp0)
REVERT: B  134 ARG cc_start: 0.8700 (ptt180) cc_final: 0.8423 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8794 (t70) cc_final: 0.8542 (t0)
REVERT: B  327 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8834 (p)
REVERT: E   43 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7685 (mtpt)
REVERT: E  213 THR cc_start: 0.8656 (p) cc_final: 0.8240 (t)
REVERT: E  217 SER cc_start: 0.8335 (m) cc_final: 0.7917 (p)
REVERT: R   57 LYS cc_start: 0.7903 (mttt) cc_final: 0.7524 (mtmm)
REVERT: R  470 LEU cc_start: 0.8053 (tt) cc_final: 0.7492 (mm)
  outliers start: 23
  outliers final: 15
  residues processed: 148
  average time/residue: 1.3347
  time to fit residues: 210.5254
Evaluate side-chains
  151 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.5362

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.144924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.106779 restraints weight = 10976.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.02
r_work: 0.3054 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9191  Z= 0.159
  Angle     :  0.528   8.376  12494  Z= 0.275
  Chirality :  0.042   0.138   1419
  Planarity :  0.004   0.041   1551
  Dihedral  :  5.677  54.641   1564
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.86 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.04 (0.25), residues: 1113
  helix:  2.99 (0.25), residues: 391
  sheet:  0.59 (0.30), residues: 269
  loop :  0.46 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.012   0.001   PHE R 435 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.008   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04199 (  461)
  hydrogen bonds       : angle       4.48343 ( 1299)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       0.98504 (    8)
  covalent geometry    : bond        0.00368 ( 9187)
  covalent geometry    : angle       0.52779 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8476 (mttt) cc_final: 0.8099 (mtmt)
REVERT: A   82 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7776 (t-170)
REVERT: A  208 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7390 (mtm180)
REVERT: A  217 CYS cc_start: 0.8281 (m) cc_final: 0.8040 (t)
REVERT: B  130 GLU cc_start: 0.8517 (mp0) cc_final: 0.8060 (mp0)
REVERT: B  134 ARG cc_start: 0.8725 (ptt180) cc_final: 0.8435 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8849 (t70) cc_final: 0.8591 (t0)
REVERT: E   43 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7908 (mmpt)
REVERT: E  174 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8784 (tt)
REVERT: E  213 THR cc_start: 0.8653 (p) cc_final: 0.8248 (t)
REVERT: R   55 GLU cc_start: 0.7315 (tp30) cc_final: 0.7088 (tp30)
REVERT: R   57 LYS cc_start: 0.8044 (mttt) cc_final: 0.7423 (pttp)
REVERT: R  436 MET cc_start: 0.8622 (mtm) cc_final: 0.8379 (mtm)
REVERT: R  470 LEU cc_start: 0.8145 (tt) cc_final: 0.7565 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 147
  average time/residue: 1.2782
  time to fit residues: 200.2829
Evaluate side-chains
  151 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  482 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN
R 472 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.146858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.108906 restraints weight = 11068.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.03
r_work: 0.3102 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9191  Z= 0.111
  Angle     :  0.492   7.670  12494  Z= 0.256
  Chirality :  0.041   0.161   1419
  Planarity :  0.003   0.040   1551
  Dihedral  :  5.528  55.237   1564
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.39 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.09 (0.26), residues: 1113
  helix:  3.08 (0.25), residues: 391
  sheet:  0.48 (0.31), residues: 270
  loop :  0.53 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.011   0.001   PHE A  74 
 TYR   0.017   0.001   TYR E 190 
 ARG   0.008   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  461)
  hydrogen bonds       : angle       4.36673 ( 1299)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.87789 (    8)
  covalent geometry    : bond        0.00244 ( 9187)
  covalent geometry    : angle       0.49212 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8451 (mttt) cc_final: 0.8065 (mtmt)
REVERT: A   82 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7710 (t-170)
REVERT: A  208 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7364 (mtm180)
REVERT: A  217 CYS cc_start: 0.8242 (m) cc_final: 0.8002 (t)
REVERT: B   13 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7631 (tp-100)
REVERT: B  130 GLU cc_start: 0.8522 (mp0) cc_final: 0.8183 (mp0)
REVERT: B  134 ARG cc_start: 0.8716 (ptt180) cc_final: 0.8457 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8806 (t70) cc_final: 0.8522 (t0)
REVERT: B  327 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8868 (p)
REVERT: E   43 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7905 (mmpt)
REVERT: E  174 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8785 (tt)
REVERT: E  213 THR cc_start: 0.8641 (p) cc_final: 0.8250 (t)
REVERT: R   57 LYS cc_start: 0.7927 (mttt) cc_final: 0.7334 (pttp)
REVERT: R  470 LEU cc_start: 0.8153 (tt) cc_final: 0.7915 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 150
  average time/residue: 1.2412
  time to fit residues: 198.5202
Evaluate side-chains
  150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  13 GLN
B  16 ASN
R 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.145987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.107872 restraints weight = 10916.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.02
r_work: 0.3070 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9191  Z= 0.132
  Angle     :  0.514   8.991  12494  Z= 0.266
  Chirality :  0.041   0.158   1419
  Planarity :  0.004   0.046   1551
  Dihedral  :  5.567  54.848   1564
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.82 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.07 (0.25), residues: 1113
  helix:  3.08 (0.25), residues: 391
  sheet:  0.51 (0.30), residues: 268
  loop :  0.47 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.013   0.001   PHE R 434 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.012   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  461)
  hydrogen bonds       : angle       4.41167 ( 1299)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       1.00812 (    8)
  covalent geometry    : bond        0.00300 ( 9187)
  covalent geometry    : angle       0.51321 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8475 (mttt) cc_final: 0.8095 (mtmt)
REVERT: A   82 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7744 (t-170)
REVERT: A  208 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7407 (mtm180)
REVERT: A  217 CYS cc_start: 0.8216 (m) cc_final: 0.8003 (t)
REVERT: B   13 GLN cc_start: 0.8008 (tm130) cc_final: 0.7636 (tp-100)
REVERT: B  130 GLU cc_start: 0.8524 (mp0) cc_final: 0.8199 (mp0)
REVERT: B  134 ARG cc_start: 0.8712 (ptt180) cc_final: 0.8449 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8832 (t70) cc_final: 0.8577 (t0)
REVERT: E   43 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7889 (mmpt)
REVERT: E  174 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8791 (tt)
REVERT: E  213 THR cc_start: 0.8638 (p) cc_final: 0.8247 (t)
REVERT: R   57 LYS cc_start: 0.7985 (mttt) cc_final: 0.7405 (pttp)
REVERT: R  436 MET cc_start: 0.8608 (mtm) cc_final: 0.8348 (mtm)
  outliers start: 20
  outliers final: 15
  residues processed: 146
  average time/residue: 1.3837
  time to fit residues: 214.9627
Evaluate side-chains
  149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0670
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.8124

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.146835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.108979 restraints weight = 11012.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.02
r_work: 0.3086 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9191  Z= 0.112
  Angle     :  0.505   8.820  12494  Z= 0.260
  Chirality :  0.041   0.156   1419
  Planarity :  0.003   0.041   1551
  Dihedral  :  5.483  55.542   1564
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.56 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.16 (0.26), residues: 1113
  helix:  3.19 (0.25), residues: 390
  sheet:  0.46 (0.31), residues: 270
  loop :  0.57 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.012   0.001   PHE R 434 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.010   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  461)
  hydrogen bonds       : angle       4.33332 ( 1299)
  SS BOND              : bond        0.00312 (    4)
  SS BOND              : angle       1.10659 (    8)
  covalent geometry    : bond        0.00246 ( 9187)
  covalent geometry    : angle       0.50430 (12486)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8459 (mttt) cc_final: 0.8077 (mtmt)
REVERT: A   82 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7728 (t-170)
REVERT: A  208 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7385 (mtm180)
REVERT: A  217 CYS cc_start: 0.8201 (m) cc_final: 0.7987 (t)
REVERT: B   13 GLN cc_start: 0.7999 (tm130) cc_final: 0.7457 (tp-100)
REVERT: B  130 GLU cc_start: 0.8521 (mp0) cc_final: 0.8190 (mp0)
REVERT: B  134 ARG cc_start: 0.8685 (ptt180) cc_final: 0.8415 (ptt-90)
REVERT: B  258 ASP cc_start: 0.8788 (t70) cc_final: 0.8509 (t0)
REVERT: B  327 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8852 (p)
REVERT: E   43 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7653 (mtpt)
REVERT: E  174 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8775 (tt)
REVERT: E  213 THR cc_start: 0.8642 (p) cc_final: 0.8260 (t)
REVERT: R   57 LYS cc_start: 0.7861 (mttt) cc_final: 0.7294 (pttp)
REVERT: R  218 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7400 (mtm110)
REVERT: R  436 MET cc_start: 0.8596 (mtm) cc_final: 0.8352 (mtm)
  outliers start: 17
  outliers final: 13
  residues processed: 141
  average time/residue: 1.2069
  time to fit residues: 181.6362
Evaluate side-chains
  147 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  441 CYS
Chi-restraints excluded: chain R residue  454 ILE
Chi-restraints excluded: chain R residue  483 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 23 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0070
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
B  16 ASN
R 472 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.110756 restraints weight = 10995.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.02
r_work: 0.3132 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9191  Z= 0.096
  Angle     :  0.489   8.682  12494  Z= 0.252
  Chirality :  0.040   0.154   1419
  Planarity :  0.003   0.041   1551
  Dihedral  :  5.361  56.535   1564
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.45 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  2.22 (0.26), residues: 1113
  helix:  3.29 (0.25), residues: 391
  sheet:  0.45 (0.31), residues: 270
  loop :  0.58 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.012   0.001   PHE R 434 
 TYR   0.018   0.001   TYR E 190 
 ARG   0.009   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  461)
  hydrogen bonds       : angle       4.22647 ( 1299)
  SS BOND              : bond        0.00289 (    4)
  SS BOND              : angle       1.08177 (    8)
  covalent geometry    : bond        0.00205 ( 9187)
  covalent geometry    : angle       0.48821 (12486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8208.55 seconds
wall clock time: 141 minutes 42.77 seconds (8502.77 seconds total)