Starting phenix.real_space_refine
on Wed Sep 17 17:06:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lyc_63523/09_2025/9lyc_63523_neut.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
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      73      5.16       5
     C    6430      2.51       5
     N    1724      2.21       5
     O    1829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10056
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2053
          Classifications: {'peptide': 273}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 259}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2589
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 1940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1940
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 2072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2072
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 263}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 431
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   SER N 127 " occ=0.94
      ... (3 atoms not shown)
      pdb=" CB  SER N 127 " occ=0.94
  Time building chain proxies: 2.52, per 1000 atoms: 0.25
  Number of scatterers: 10056
  At special positions: 0
  Unit cell: (79.872, 106.496, 146.432, 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      73     16.00
     O    1829      8.00
     N    1724      7.00
     C    6430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 177 " - pdb=" SG  CYS D 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 0.93
  Conformation dependent library (CDL) restraints added in 398.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2452

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      50.5% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 68
      removed outlier: 3.724A  pdb=" N   VAL A  45 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   VAL A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A  60 " --> pdb=" O   CYS A  56 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 101
      removed outlier: 3.752A  pdb=" N   LEU A  78 " --> pdb=" O   PRO A  74 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A  79 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 140
    Processing helix  chain 'A' and resid 146 through 168
      removed outlier: 3.699A  pdb=" N   VAL A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.800A  pdb=" N   ALA A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 232
    Processing helix  chain 'A' and resid 242 through 270
      Proline residue:  A 262  - end of helix
    Processing helix  chain 'A' and resid 276 through 282
      removed outlier: 4.226A  pdb=" N   TYR A 280 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   THR A 282 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 298
      removed outlier: 3.519A  pdb=" N   THR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      Proline residue:  A 294  - end of helix
    Processing helix  chain 'A' and resid 301 through 312
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.511A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.749A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 40
      removed outlier: 4.428A  pdb=" N   GLU C  15 " --> pdb=" O   ASP C  11 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS C  32 " --> pdb=" O   LYS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 60
    Processing helix  chain 'C' and resid 213 through 217
      removed outlier: 3.769A  pdb=" N   LYS C 216 " --> pdb=" O   GLN C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 239
      removed outlier: 3.722A  pdb=" N   GLN C 236 " --> pdb=" O   LYS C 233 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASN C 239 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 279
      removed outlier: 3.843A  pdb=" N   ALA C 268 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 304
    Processing helix  chain 'C' and resid 307 through 312
      removed outlier: 4.454A  pdb=" N   TYR C 311 " --> pdb=" O   LYS C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 352
      removed outlier: 3.633A  pdb=" N   ARG C 342 " --> pdb=" O   LYS C 338 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE C 348 " --> pdb=" O   GLU C 344 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER C 352 " --> pdb=" O   ILE C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 391
      removed outlier: 3.508A  pdb=" N   ARG C 374 " --> pdb=" O   GLU C 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 68
      removed outlier: 3.577A  pdb=" N   THR D  68 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 102
      removed outlier: 3.887A  pdb=" N   LEU D  78 " --> pdb=" O   PRO D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 143
      removed outlier: 3.657A  pdb=" N   SER D 109 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR D 143 " --> pdb=" O   TYR D 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 164
      removed outlier: 3.564A  pdb=" N   ARG D 152 " --> pdb=" O   THR D 148 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR D 154 " --> pdb=" O   VAL D 150 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU D 159 " --> pdb=" O   VAL D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 170
    Processing helix  chain 'D' and resid 176 through 181
      removed outlier: 3.619A  pdb=" N   GLY D 180 " --> pdb=" O   ASN D 176 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LEU D 181 " --> pdb=" O   CYS D 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 176 through 181'
    Processing helix  chain 'D' and resid 191 through 223
    Processing helix  chain 'D' and resid 223 through 230
    Processing helix  chain 'D' and resid 242 through 270
      removed outlier: 4.099A  pdb=" N   THR D 248 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   LEU D 249 " --> pdb=" O   GLY D 245 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA D 250 " --> pdb=" O   ILE D 246 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL D 251 " --> pdb=" O   ALA D 247 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   CYS D 259 " --> pdb=" O   ALA D 255 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU D 261 " --> pdb=" O   ALA D 257 " (cutoff:3.500A)
      Proline residue:  D 262  - end of helix
      removed outlier: 3.950A  pdb=" N   TYR D 266 " --> pdb=" O   PRO D 262 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU D 268 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 298
      removed outlier: 3.716A  pdb=" N   THR D 279 " --> pdb=" O   PRO D 275 " (cutoff:3.500A)
      Proline residue:  D 285  - end of helix
      Proline residue:  D 294  - end of helix
    Processing helix  chain 'D' and resid 301 through 314
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.513A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.671A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.607A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.252A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.909A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.405A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.570A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.212A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.615A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.341A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 211
      removed outlier: 3.762A  pdb=" N   PHE C 208 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   HIS C  41 " --> pdb=" O   HIS C 220 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   PHE C 222 " --> pdb=" O   HIS C  41 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU C  43 " --> pdb=" O   PHE C 222 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL C 224 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 8.288A  pdb=" N   LEU C  45 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ARG C  42 " --> pdb=" O   ALA C 243 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   ILE C 245 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LEU C  44 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL C 247 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   ALA C 249 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   ILE C 244 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   PHE C 290 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   PHE C 246 " --> pdb=" O   PHE C 290 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ASN C 292 " --> pdb=" O   PHE C 246 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   VAL C 248 " --> pdb=" O   ASN C 292 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.797A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 5.895A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1683 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: 1.61

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2391
        1.33 -     1.45: 2127
        1.45 -     1.57: 5643
        1.57 -     1.70: 0
        1.70 -     1.82: 101
  Bond restraints: 10262
  Sorted by residual:
  bond pdb=" CA  LYS B  89 "
       pdb=" C   LYS B  89 "
    ideal  model  delta    sigma   weight residual
    1.522  1.472  0.049 1.22e-02 6.72e+03 1.65e+01
  bond pdb=" N   VAL B  90 "
       pdb=" CA  VAL B  90 "
    ideal  model  delta    sigma   weight residual
    1.459  1.429  0.030 1.25e-02 6.40e+03 5.62e+00
  bond pdb=" CA  VAL B  90 "
       pdb=" CB  VAL B  90 "
    ideal  model  delta    sigma   weight residual
    1.540  1.510  0.031 1.36e-02 5.41e+03 5.03e+00
  bond pdb=" C   HIS B  91 "
       pdb=" O   HIS B  91 "
    ideal  model  delta    sigma   weight residual
    1.235  1.209  0.026 1.18e-02 7.18e+03 4.90e+00
  bond pdb=" C   LYS B  89 "
       pdb=" N   VAL B  90 "
    ideal  model  delta    sigma   weight residual
    1.332  1.304  0.028 1.36e-02 5.41e+03 4.15e+00
  ... (remaining 10257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 13767
        2.42 -     4.84: 154
        4.84 -     7.26: 27
        7.26 -     9.68: 9
        9.68 -    12.10: 2
  Bond angle restraints: 13959
  Sorted by residual:
  angle pdb=" N   LYS B  89 "
        pdb=" CA  LYS B  89 "
        pdb=" C   LYS B  89 "
      ideal   model   delta    sigma   weight residual
     109.40  102.65    6.75 1.63e+00 3.76e-01 1.71e+01
  angle pdb=" CA  PRO A  74 "
        pdb=" N   PRO A  74 "
        pdb=" CD  PRO A  74 "
      ideal   model   delta    sigma   weight residual
     112.00  106.77    5.23 1.40e+00 5.10e-01 1.40e+01
  angle pdb=" CA  MET D 118 "
        pdb=" CB  MET D 118 "
        pdb=" CG  MET D 118 "
      ideal   model   delta    sigma   weight residual
     114.10  121.25   -7.15 2.00e+00 2.50e-01 1.28e+01
  angle pdb=" C   HIS B  91 "
        pdb=" N   ALA B  92 "
        pdb=" CA  ALA B  92 "
      ideal   model   delta    sigma   weight residual
     122.77  127.89   -5.12 1.48e+00 4.57e-01 1.20e+01
  angle pdb=" CA  LEU D  95 "
        pdb=" CB  LEU D  95 "
        pdb=" CG  LEU D  95 "
      ideal   model   delta    sigma   weight residual
     116.30  128.40  -12.10 3.50e+00 8.16e-02 1.19e+01
  ... (remaining 13954 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 5200
       15.92 -    31.84: 644
       31.84 -    47.76: 194
       47.76 -    63.69: 34
       63.69 -    79.61: 9
  Dihedral angle restraints: 6081
    sinusoidal: 2280
      harmonic: 3801
  Sorted by residual:
  dihedral pdb=" CA  LYS G  20 "
           pdb=" C   LYS G  20 "
           pdb=" N   MET G  21 "
           pdb=" CA  MET G  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.73   21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  TRP B 297 "
           pdb=" C   TRP B 297 "
           pdb=" N   ASP B 298 "
           pdb=" CA  ASP B 298 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.52  -20.48     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASP D 179 "
           pdb=" C   ASP D 179 "
           pdb=" N   GLY D 180 "
           pdb=" CA  GLY D 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.32   19.68     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6078 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1096
       0.036 -    0.072: 395
       0.072 -    0.108: 107
       0.108 -    0.144: 31
       0.144 -    0.180: 8
  Chirality restraints: 1637
  Sorted by residual:
  chirality pdb=" CB  VAL B  90 "
            pdb=" CA  VAL B  90 "
            pdb=" CG1 VAL B  90 "
            pdb=" CG2 VAL B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" CB  VAL A 115 "
            pdb=" CA  VAL A 115 "
            pdb=" CG1 VAL A 115 "
            pdb=" CG2 VAL A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.30e-01
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.74e-01
  ... (remaining 1634 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  73 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.25e+01
        pdb=" N   PRO A  74 "    0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 258 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.14e+00
        pdb=" C   ASP B 258 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASP B 258 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN B 259 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 293 "   -0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO D 294 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 294 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 294 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 110
        2.61 -     3.18: 8800
        3.18 -     3.75: 16027
        3.75 -     4.33: 20680
        4.33 -     4.90: 34526
  Nonbonded interactions: 80143
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D  86 "
            pdb=" OG  SER D 290 "
     model   vdw
     2.034 3.040
  nonbonded pdb=" OD1 ASP A  86 "
            pdb=" OG  SER A 290 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OG  SER N  52 "
            pdb=" OG  SER N  57 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" ND2 ASN B  88 "
            pdb=" OE1 GLN C  19 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" OD1 ASP A 271 "
            pdb=" OG  SER A 274 "
     model   vdw
     2.197 3.040
  ... (remaining 80138 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 143 or (resid 144 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 145 through 312))
  selection = (chain 'D' and (resid 35 through 232 or resid 241 through 312))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.740
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
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      :  0.004   0.083  10266  Z= 0.174
  Angle     :  0.685  12.097  13967  Z= 0.353
  Chirality :  0.042   0.180   1637
  Planarity :  0.005   0.119   1761
  Dihedral  : 15.516  79.607   3617
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 24.06 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.24), residues: 1292
  helix:  1.67 (0.21), residues: 610
  sheet:  0.69 (0.34), residues: 233
  loop : -0.74 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 317 
 TYR   0.014   0.001   TYR D 266 
 PHE   0.020   0.002   PHE A  97 
 TRP   0.028   0.002   TRP C 281 
 HIS   0.007   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10262)
  covalent geometry    : angle       0.68411 (13959)
  SS BOND              : bond        0.00116 (    4)
  SS BOND              : angle       1.36415 (    8)
  hydrogen bonds       : bond        0.14119 (  577)
  hydrogen bonds       : angle       5.32395 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 309
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.7890 (t) cc_final: 0.7581 (p)
REVERT: B    4 LEU cc_start: 0.7395 (tp) cc_final: 0.7119 (tt)
REVERT: B   19 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7526 (ttp80)
REVERT: B   25 CYS cc_start: 0.7804 (m) cc_final: 0.7508 (m)
REVERT: B   50 THR cc_start: 0.8365 (m) cc_final: 0.7916 (t)
REVERT: B  188 MET cc_start: 0.7986 (mmm) cc_final: 0.7458 (mmm)
REVERT: B  217 MET cc_start: 0.7272 (ptt) cc_final: 0.7061 (ptt)
REVERT: B  230 ASN cc_start: 0.8254 (m-40) cc_final: 0.7911 (m110)
REVERT: B  246 ASP cc_start: 0.7833 (m-30) cc_final: 0.7549 (m-30)
REVERT: B  253 PHE cc_start: 0.8465 (m-80) cc_final: 0.8198 (m-80)
REVERT: B  259 GLN cc_start: 0.7795 (pt0) cc_final: 0.7547 (pt0)
REVERT: B  262 MET cc_start: 0.7810 (tpt) cc_final: 0.7480 (mtp)
REVERT: B  291 ASP cc_start: 0.8173 (p0) cc_final: 0.7735 (p0)
REVERT: B  296 VAL cc_start: 0.8153 (t) cc_final: 0.7924 (p)
REVERT: B  297 TRP cc_start: 0.8401 (m100) cc_final: 0.8108 (m100)
REVERT: B  323 ASP cc_start: 0.8356 (p0) cc_final: 0.7537 (p0)
REVERT: C  228 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7342 (mtp180)
REVERT: C  230 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: C  242 THR cc_start: 0.8684 (m) cc_final: 0.8465 (t)
REVERT: C  381 ASP cc_start: 0.7702 (t0) cc_final: 0.7499 (t0)
REVERT: C  389 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7362 (ttt-90)
REVERT: D   48 CYS cc_start: 0.5783 (t) cc_final: 0.5451 (t)
REVERT: D   97 PHE cc_start: 0.6446 (t80) cc_final: 0.6045 (t80)
REVERT: D  130 ILE cc_start: 0.8489 (mt) cc_final: 0.8126 (tt)
REVERT: G   29 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7538 (mmmt)
REVERT: N   25 SER cc_start: 0.8285 (p) cc_final: 0.8012 (m)
REVERT: N   35 ASN cc_start: 0.7517 (m-40) cc_final: 0.7283 (m-40)
REVERT: N   38 ARG cc_start: 0.7572 (ptt90) cc_final: 0.6587 (ttp-170)
REVERT: N   87 LYS cc_start: 0.7963 (mttt) cc_final: 0.7650 (mtmm)
REVERT: N  118 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8495 (ttm170)
REVERT: N  120 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7505 (mm-40)
  outliers start: 8
  outliers final: 4
  residues processed: 310
  average time/residue: 0.1124
  time to fit residues: 47.1827
Evaluate side-chains
  267 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 263
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain C residue   20 ARG
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain D residue  153 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0030
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 119 ASN
B 176 GLN
B 239 ASN
B 295 ASN
C  23 ASN
** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 387 HIS
N  74 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.159427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.138422 restraints weight = 15188.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 2.53
r_work: 0.3694 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10266  Z= 0.151
  Angle     :  0.619  10.739  13967  Z= 0.316
  Chirality :  0.042   0.165   1637
  Planarity :  0.005   0.075   1761
  Dihedral  :  4.868  54.861   1423
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.25 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.24), residues: 1292
  helix:  2.05 (0.21), residues: 615
  sheet:  0.81 (0.35), residues: 225
  loop : -0.82 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 137 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.016   0.002   PHE A  97 
 TRP   0.015   0.002   TRP D 309 
 HIS   0.005   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10262)
  covalent geometry    : angle       0.61844 (13959)
  SS BOND              : bond        0.00366 (    4)
  SS BOND              : angle       1.09455 (    8)
  hydrogen bonds       : bond        0.04851 (  577)
  hydrogen bonds       : angle       4.43425 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 276
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8108 (t) cc_final: 0.7865 (p)
REVERT: A  291 MET cc_start: 0.7337 (ttm) cc_final: 0.6979 (ttm)
REVERT: B   18 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7376 (tt)
REVERT: B   19 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7673 (ttp-110)
REVERT: B   25 CYS cc_start: 0.7976 (m) cc_final: 0.7508 (t)
REVERT: B   76 ASP cc_start: 0.7497 (p0) cc_final: 0.7063 (p0)
REVERT: B  137 ARG cc_start: 0.7504 (tpp80) cc_final: 0.6998 (tpp80)
REVERT: B  188 MET cc_start: 0.7953 (mmm) cc_final: 0.7398 (mmm)
REVERT: B  230 ASN cc_start: 0.8214 (m-40) cc_final: 0.7920 (m110)
REVERT: B  237 ASN cc_start: 0.8233 (p0) cc_final: 0.8031 (p0)
REVERT: B  246 ASP cc_start: 0.7948 (m-30) cc_final: 0.7633 (m-30)
REVERT: B  253 PHE cc_start: 0.8421 (m-80) cc_final: 0.8182 (m-80)
REVERT: B  262 MET cc_start: 0.7802 (tpt) cc_final: 0.7486 (mmm)
REVERT: B  273 ILE cc_start: 0.8260 (mp) cc_final: 0.8057 (mt)
REVERT: B  291 ASP cc_start: 0.8348 (p0) cc_final: 0.7954 (p0)
REVERT: B  323 ASP cc_start: 0.8510 (p0) cc_final: 0.7828 (p0)
REVERT: C   21 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6620 (tm-30)
REVERT: C   38 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.7050 (ttm-80)
REVERT: C   43 LEU cc_start: 0.8368 (mt) cc_final: 0.8160 (mp)
REVERT: C  218 ASN cc_start: 0.7632 (m-40) cc_final: 0.7352 (m-40)
REVERT: C  228 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7882 (mtp-110)
REVERT: C  230 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7350 (mt-10)
REVERT: C  279 ASN cc_start: 0.8377 (t0) cc_final: 0.8087 (t0)
REVERT: C  342 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7593 (ttt-90)
REVERT: D   79 VAL cc_start: 0.8056 (t) cc_final: 0.7826 (t)
REVERT: D  292 ILE cc_start: 0.7814 (tt) cc_final: 0.7421 (tt)
REVERT: N   35 ASN cc_start: 0.7896 (m-40) cc_final: 0.7636 (m110)
REVERT: N  120 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7734 (mm-40)
  outliers start: 41
  outliers final: 18
  residues processed: 304
  average time/residue: 0.1072
  time to fit residues: 44.0656
Evaluate side-chains
  292 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 272
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   20 ARG
Chi-restraints excluded: chain C residue   21 GLU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0770
   chunk 65 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 ASN
B 119 ASN
B 176 GLN
B 239 ASN
C  23 ASN
C 377 ASN
** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 123 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.156305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135247 restraints weight = 15204.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 2.53
r_work: 0.3645 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10266  Z= 0.152
  Angle     :  0.609  12.034  13967  Z= 0.307
  Chirality :  0.042   0.184   1637
  Planarity :  0.004   0.062   1761
  Dihedral  :  4.563  48.307   1419
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.75 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.24), residues: 1292
  helix:  2.16 (0.21), residues: 616
  sheet:  0.67 (0.34), residues: 229
  loop : -0.81 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 251 
 TYR   0.011   0.001   TYR N  60 
 PHE   0.015   0.002   PHE B 222 
 TRP   0.012   0.001   TRP D 309 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10262)
  covalent geometry    : angle       0.60861 (13959)
  SS BOND              : bond        0.00403 (    4)
  SS BOND              : angle       0.75565 (    8)
  hydrogen bonds       : bond        0.04498 (  577)
  hydrogen bonds       : angle       4.32229 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 291
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8163 (t) cc_final: 0.7934 (p)
REVERT: A  157 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (mt)
REVERT: B   19 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7729 (ttp80)
REVERT: B   25 CYS cc_start: 0.7986 (m) cc_final: 0.7768 (m)
REVERT: B  118 ASP cc_start: 0.7366 (p0) cc_final: 0.7094 (p0)
REVERT: B  119 ASN cc_start: 0.7889 (m-40) cc_final: 0.7550 (m110)
REVERT: B  137 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7265 (tpp80)
REVERT: B  188 MET cc_start: 0.7939 (mmm) cc_final: 0.7555 (mmm)
REVERT: B  230 ASN cc_start: 0.8200 (m-40) cc_final: 0.7907 (m110)
REVERT: B  237 ASN cc_start: 0.8247 (p0) cc_final: 0.7996 (p0)
REVERT: B  246 ASP cc_start: 0.7955 (m-30) cc_final: 0.7574 (m-30)
REVERT: B  262 MET cc_start: 0.7939 (tpt) cc_final: 0.7537 (mmm)
REVERT: B  273 ILE cc_start: 0.8302 (mp) cc_final: 0.8076 (mt)
REVERT: B  297 TRP cc_start: 0.8464 (m100) cc_final: 0.8098 (m100)
REVERT: C   38 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7202 (ttm-80)
REVERT: C  218 ASN cc_start: 0.7767 (m-40) cc_final: 0.7354 (m-40)
REVERT: C  219 PHE cc_start: 0.7637 (m-10) cc_final: 0.7256 (m-10)
REVERT: C  228 ARG cc_start: 0.8287 (mtm180) cc_final: 0.8049 (mtm110)
REVERT: C  274 ASP cc_start: 0.8026 (t70) cc_final: 0.7683 (t0)
REVERT: C  279 ASN cc_start: 0.8443 (t0) cc_final: 0.8112 (t0)
REVERT: C  289 LEU cc_start: 0.7809 (tp) cc_final: 0.7547 (tp)
REVERT: C  342 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7628 (ttt-90)
REVERT: C  381 ASP cc_start: 0.7341 (t0) cc_final: 0.7082 (t0)
REVERT: D  289 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6893 (t0)
REVERT: G   50 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7529 (mt)
REVERT: N   35 ASN cc_start: 0.8070 (m-40) cc_final: 0.7799 (m110)
REVERT: N   38 ARG cc_start: 0.7620 (ptt90) cc_final: 0.7078 (ptt90)
REVERT: N  120 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7628 (mm-40)
  outliers start: 52
  outliers final: 27
  residues processed: 316
  average time/residue: 0.1035
  time to fit residues: 44.2768
Evaluate side-chains
  312 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  293 LYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  289 ASN
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0470
   chunk 36 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 239 ASN
C 377 ASN
** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.152974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.131987 restraints weight = 15080.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.49
r_work: 0.3589 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10266  Z= 0.168
  Angle     :  0.616   9.294  13967  Z= 0.313
  Chirality :  0.042   0.162   1637
  Planarity :  0.004   0.062   1761
  Dihedral  :  4.362  20.525   1415
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 22.57 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.24), residues: 1292
  helix:  1.97 (0.21), residues: 620
  sheet:  0.56 (0.33), residues: 223
  loop : -0.80 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 251 
 TYR   0.013   0.001   TYR N  60 
 PHE   0.015   0.002   PHE C 376 
 TRP   0.013   0.002   TRP C 234 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10262)
  covalent geometry    : angle       0.61571 (13959)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       0.78890 (    8)
  hydrogen bonds       : bond        0.04502 (  577)
  hydrogen bonds       : angle       4.23978 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 299
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 VAL cc_start: 0.8224 (t) cc_final: 0.8019 (p)
REVERT: A  157 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8295 (mt)
REVERT: A  225 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7227 (mp10)
REVERT: B   19 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7594 (ttp80)
REVERT: B  126 LEU cc_start: 0.7668 (mt) cc_final: 0.7457 (mt)
REVERT: B  137 ARG cc_start: 0.7961 (tpp80) cc_final: 0.7419 (tpp80)
REVERT: B  150 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7799 (mmt-90)
REVERT: B  188 MET cc_start: 0.7905 (mmm) cc_final: 0.7417 (mmm)
REVERT: B  212 ASP cc_start: 0.7743 (p0) cc_final: 0.6928 (p0)
REVERT: B  230 ASN cc_start: 0.8217 (m-40) cc_final: 0.7895 (m110)
REVERT: B  237 ASN cc_start: 0.8210 (p0) cc_final: 0.7967 (p0)
REVERT: B  246 ASP cc_start: 0.7969 (m-30) cc_final: 0.7581 (m-30)
REVERT: B  262 MET cc_start: 0.7924 (tpt) cc_final: 0.7486 (mmm)
REVERT: B  291 ASP cc_start: 0.8244 (p0) cc_final: 0.7932 (p0)
REVERT: B  323 ASP cc_start: 0.8504 (p0) cc_final: 0.7800 (p0)
REVERT: C   20 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7544 (mtt-85)
REVERT: C   21 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6726 (tm-30)
REVERT: C   31 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7952 (mm-40)
REVERT: C   34 LYS cc_start: 0.8290 (tttp) cc_final: 0.7759 (tttp)
REVERT: C   38 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7346 (ttm-80)
REVERT: C  218 ASN cc_start: 0.7919 (m-40) cc_final: 0.7437 (m-40)
REVERT: C  279 ASN cc_start: 0.8478 (t0) cc_final: 0.8187 (t0)
REVERT: C  289 LEU cc_start: 0.7857 (tp) cc_final: 0.7600 (tp)
REVERT: C  342 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7638 (ttt-90)
REVERT: C  376 PHE cc_start: 0.8074 (t80) cc_final: 0.7696 (t80)
REVERT: D   82 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6995 (tp)
REVERT: D  289 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.6901 (t0)
REVERT: G   50 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7684 (mt)
REVERT: N   35 ASN cc_start: 0.8128 (m-40) cc_final: 0.7847 (m110)
REVERT: N   38 ARG cc_start: 0.7848 (ptt90) cc_final: 0.7318 (ptt90)
REVERT: N   39 GLN cc_start: 0.8233 (tp40) cc_final: 0.7753 (tt0)
REVERT: N  120 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7499 (mm-40)
  outliers start: 55
  outliers final: 32
  residues processed: 330
  average time/residue: 0.1087
  time to fit residues: 48.3479
Evaluate side-chains
  333 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 295
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   21 GLU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  293 LYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  289 ASN
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 103 optimal weight:    0.0060
   chunk 14 optimal weight:    5.9990
   chunk 100 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 239 ASN
C 377 ASN
** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.153092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.131475 restraints weight = 15091.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.51
r_work: 0.3569 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10266  Z= 0.140
  Angle     :  0.594   9.365  13967  Z= 0.300
  Chirality :  0.041   0.156   1637
  Planarity :  0.004   0.060   1761
  Dihedral  :  4.286  21.113   1415
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.81 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.24), residues: 1292
  helix:  2.03 (0.21), residues: 621
  sheet:  0.48 (0.34), residues: 218
  loop : -0.86 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 251 
 TYR   0.010   0.001   TYR N  60 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.026   0.001   TRP C 281 
 HIS   0.003   0.001   HIS A 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10262)
  covalent geometry    : angle       0.59420 (13959)
  SS BOND              : bond        0.00625 (    4)
  SS BOND              : angle       0.55725 (    8)
  hydrogen bonds       : bond        0.04282 (  577)
  hydrogen bonds       : angle       4.15386 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 296
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8554 (mt) cc_final: 0.8314 (mp)
REVERT: A  157 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (mt)
REVERT: A  225 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7235 (mp10)
REVERT: B   19 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7718 (ttp80)
REVERT: B   49 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.8162 (mpt180)
REVERT: B  150 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7835 (mmt-90)
REVERT: B  188 MET cc_start: 0.7882 (mmm) cc_final: 0.7336 (mmm)
REVERT: B  217 MET cc_start: 0.7727 (pmm) cc_final: 0.7436 (pmm)
REVERT: B  230 ASN cc_start: 0.8205 (m-40) cc_final: 0.7886 (m110)
REVERT: B  237 ASN cc_start: 0.8206 (p0) cc_final: 0.7997 (p0)
REVERT: B  246 ASP cc_start: 0.7966 (m-30) cc_final: 0.7578 (m-30)
REVERT: B  262 MET cc_start: 0.7929 (tpt) cc_final: 0.7444 (mmm)
REVERT: B  291 ASP cc_start: 0.8212 (p0) cc_final: 0.7612 (p0)
REVERT: C   21 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6801 (tm-30)
REVERT: C   31 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7824 (mm-40)
REVERT: C   33 ASP cc_start: 0.7596 (p0) cc_final: 0.7199 (p0)
REVERT: C   34 LYS cc_start: 0.8319 (tttp) cc_final: 0.7711 (tttp)
REVERT: C   38 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7357 (ttm-80)
REVERT: C   60 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3916 (ttm)
REVERT: C  218 ASN cc_start: 0.7849 (m-40) cc_final: 0.7563 (m-40)
REVERT: C  219 PHE cc_start: 0.8095 (m-10) cc_final: 0.7797 (m-80)
REVERT: C  274 ASP cc_start: 0.8032 (t0) cc_final: 0.7813 (t0)
REVERT: C  279 ASN cc_start: 0.8483 (t0) cc_final: 0.8258 (t0)
REVERT: C  289 LEU cc_start: 0.7812 (tp) cc_final: 0.7561 (tp)
REVERT: C  342 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7676 (ttt-90)
REVERT: C  360 TYR cc_start: 0.8172 (m-80) cc_final: 0.7870 (m-80)
REVERT: C  376 PHE cc_start: 0.8086 (t80) cc_final: 0.7736 (t80)
REVERT: C  381 ASP cc_start: 0.7440 (t0) cc_final: 0.7210 (t0)
REVERT: D  172 VAL cc_start: 0.7437 (t) cc_final: 0.7148 (p)
REVERT: G   50 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7774 (mt)
REVERT: N   35 ASN cc_start: 0.8118 (m-40) cc_final: 0.7819 (m110)
REVERT: N   38 ARG cc_start: 0.7657 (ptt90) cc_final: 0.7203 (ptt90)
REVERT: N   39 GLN cc_start: 0.8195 (tp40) cc_final: 0.7747 (tt0)
REVERT: N  120 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7510 (mm-40)
  outliers start: 53
  outliers final: 33
  residues processed: 322
  average time/residue: 0.1109
  time to fit residues: 48.0279
Evaluate side-chains
  325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 287
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   21 GLU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  293 LYS
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 72 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
C 377 ASN
** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.150068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.128391 restraints weight = 15071.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.44
r_work: 0.3545 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  10266  Z= 0.214
  Angle     :  0.654  10.423  13967  Z= 0.332
  Chirality :  0.043   0.194   1637
  Planarity :  0.004   0.061   1761
  Dihedral  :  4.495  20.727   1415
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 24.25 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.23), residues: 1292
  helix:  1.80 (0.20), residues: 622
  sheet:  0.29 (0.33), residues: 229
  loop : -0.87 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 251 
 TYR   0.019   0.002   TYR N  32 
 PHE   0.023   0.002   PHE D 101 
 TRP   0.020   0.002   TRP C 281 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (10262)
  covalent geometry    : angle       0.65446 (13959)
  SS BOND              : bond        0.00555 (    4)
  SS BOND              : angle       0.61364 (    8)
  hydrogen bonds       : bond        0.04759 (  577)
  hydrogen bonds       : angle       4.30151 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 304
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8065 (tmm) cc_final: 0.7736 (tmm)
REVERT: A   77 LEU cc_start: 0.8591 (mt) cc_final: 0.8341 (mp)
REVERT: A  157 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8392 (mt)
REVERT: A  225 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7319 (mp10)
REVERT: B   19 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7769 (ttp80)
REVERT: B   49 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8207 (mpt180)
REVERT: B  101 MET cc_start: 0.8500 (mtp) cc_final: 0.8270 (mtp)
REVERT: B  118 ASP cc_start: 0.7724 (p0) cc_final: 0.7509 (p0)
REVERT: B  188 MET cc_start: 0.7785 (mmm) cc_final: 0.7468 (mmm)
REVERT: B  212 ASP cc_start: 0.7538 (p0) cc_final: 0.7126 (p0)
REVERT: B  217 MET cc_start: 0.7777 (pmm) cc_final: 0.7546 (pmm)
REVERT: B  230 ASN cc_start: 0.8178 (m-40) cc_final: 0.7854 (m110)
REVERT: B  237 ASN cc_start: 0.8279 (p0) cc_final: 0.8049 (p0)
REVERT: B  246 ASP cc_start: 0.8004 (m-30) cc_final: 0.7589 (m-30)
REVERT: B  262 MET cc_start: 0.7918 (tpt) cc_final: 0.7522 (mmm)
REVERT: B  283 ARG cc_start: 0.8460 (tpt170) cc_final: 0.8108 (tpt90)
REVERT: B  300 LEU cc_start: 0.4527 (OUTLIER) cc_final: 0.4023 (mp)
REVERT: C   20 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7468 (mpt-90)
REVERT: C   31 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7678 (mm-40)
REVERT: C   33 ASP cc_start: 0.7542 (p0) cc_final: 0.7160 (p0)
REVERT: C   60 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3808 (ttm)
REVERT: C  208 PHE cc_start: 0.8537 (m-10) cc_final: 0.8314 (m-10)
REVERT: C  218 ASN cc_start: 0.7798 (m-40) cc_final: 0.7392 (m-40)
REVERT: C  219 PHE cc_start: 0.8168 (m-10) cc_final: 0.7876 (m-80)
REVERT: C  274 ASP cc_start: 0.8011 (t0) cc_final: 0.7767 (t0)
REVERT: C  279 ASN cc_start: 0.8502 (t0) cc_final: 0.8183 (t0)
REVERT: C  289 LEU cc_start: 0.7933 (tp) cc_final: 0.7703 (tp)
REVERT: C  376 PHE cc_start: 0.8271 (t80) cc_final: 0.7710 (t80)
REVERT: D   82 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7367 (tp)
REVERT: D  183 THR cc_start: 0.7259 (t) cc_final: 0.6820 (p)
REVERT: N   38 ARG cc_start: 0.7897 (ptt90) cc_final: 0.7439 (ptt90)
REVERT: N   39 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7737 (tt0)
REVERT: N   65 LYS cc_start: 0.8249 (tptp) cc_final: 0.8035 (tppp)
REVERT: N  120 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7651 (mm-40)
  outliers start: 60
  outliers final: 40
  residues processed: 333
  average time/residue: 0.1139
  time to fit residues: 50.8843
Evaluate side-chains
  339 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 293
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 118 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 108 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   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  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 HIS
C 377 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.129409 restraints weight = 14991.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.50
r_work: 0.3547 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10266  Z= 0.154
  Angle     :  0.626  10.332  13967  Z= 0.319
  Chirality :  0.042   0.169   1637
  Planarity :  0.004   0.058   1761
  Dihedral  :  4.372  18.893   1415
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 26.22 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.23), residues: 1292
  helix:  1.92 (0.21), residues: 618
  sheet:  0.30 (0.34), residues: 221
  loop : -0.91 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 251 
 TYR   0.011   0.001   TYR A 213 
 PHE   0.020   0.001   PHE D 101 
 TRP   0.015   0.002   TRP C 281 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10262)
  covalent geometry    : angle       0.62594 (13959)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       0.40089 (    8)
  hydrogen bonds       : bond        0.04423 (  577)
  hydrogen bonds       : angle       4.24018 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 296
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8074 (tmm) cc_final: 0.7724 (tmm)
REVERT: A   77 LEU cc_start: 0.8550 (mt) cc_final: 0.8294 (mp)
REVERT: A  127 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8022 (mp)
REVERT: A  157 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8334 (mt)
REVERT: A  177 CYS cc_start: 0.5287 (t) cc_final: 0.4906 (t)
REVERT: A  225 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7328 (mp10)
REVERT: B   19 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7711 (ttp80)
REVERT: B  118 ASP cc_start: 0.7753 (p0) cc_final: 0.7545 (p0)
REVERT: B  150 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7816 (mmt-90)
REVERT: B  188 MET cc_start: 0.7831 (mmm) cc_final: 0.7424 (mmm)
REVERT: B  212 ASP cc_start: 0.7639 (p0) cc_final: 0.7220 (p0)
REVERT: B  217 MET cc_start: 0.7888 (pmm) cc_final: 0.7591 (pmm)
REVERT: B  230 ASN cc_start: 0.8231 (m-40) cc_final: 0.7909 (m110)
REVERT: B  246 ASP cc_start: 0.8052 (m-30) cc_final: 0.7612 (m-30)
REVERT: B  262 MET cc_start: 0.7949 (tpt) cc_final: 0.7504 (mmm)
REVERT: C   20 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7431 (mpt-90)
REVERT: C   29 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7803 (tp-100)
REVERT: C   31 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7697 (mm-40)
REVERT: C   33 ASP cc_start: 0.7575 (p0) cc_final: 0.7148 (p0)
REVERT: C   60 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.3852 (ttm)
REVERT: C  218 ASN cc_start: 0.7702 (m-40) cc_final: 0.7347 (m-40)
REVERT: C  219 PHE cc_start: 0.8109 (m-10) cc_final: 0.7822 (m-80)
REVERT: C  274 ASP cc_start: 0.8014 (t0) cc_final: 0.7773 (t0)
REVERT: C  279 ASN cc_start: 0.8475 (t0) cc_final: 0.8215 (t0)
REVERT: C  289 LEU cc_start: 0.7855 (tp) cc_final: 0.7586 (tp)
REVERT: C  342 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7672 (ttt-90)
REVERT: C  376 PHE cc_start: 0.8195 (t80) cc_final: 0.7714 (t80)
REVERT: N   38 ARG cc_start: 0.7721 (ptt90) cc_final: 0.7492 (ptt90)
REVERT: N   39 GLN cc_start: 0.8203 (tp40) cc_final: 0.7779 (tt0)
REVERT: N   65 LYS cc_start: 0.8241 (tptp) cc_final: 0.7983 (tppp)
REVERT: N  120 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7647 (mm-40)
  outliers start: 49
  outliers final: 36
  residues processed: 318
  average time/residue: 0.1020
  time to fit residues: 44.1537
Evaluate side-chains
  329 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 289
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 377 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.150377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.129179 restraints weight = 15038.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.48
r_work: 0.3550 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  10266  Z= 0.161
  Angle     :  0.628  10.327  13967  Z= 0.320
  Chirality :  0.042   0.154   1637
  Planarity :  0.004   0.057   1761
  Dihedral  :  4.374  19.453   1415
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.40 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.24), residues: 1292
  helix:  1.92 (0.21), residues: 618
  sheet:  0.30 (0.35), residues: 214
  loop : -0.87 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.011   0.001   TYR N  60 
 PHE   0.020   0.002   PHE D 101 
 TRP   0.016   0.002   TRP C 281 
 HIS   0.008   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10262)
  covalent geometry    : angle       0.62804 (13959)
  SS BOND              : bond        0.00206 (    4)
  SS BOND              : angle       0.46232 (    8)
  hydrogen bonds       : bond        0.04442 (  577)
  hydrogen bonds       : angle       4.26681 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 293
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8064 (tmm) cc_final: 0.7700 (tmm)
REVERT: A   77 LEU cc_start: 0.8543 (mt) cc_final: 0.8301 (mp)
REVERT: A  127 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (mp)
REVERT: A  157 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8324 (mt)
REVERT: A  177 CYS cc_start: 0.5273 (t) cc_final: 0.4948 (t)
REVERT: A  225 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7366 (mp10)
REVERT: B   16 ASN cc_start: 0.7761 (t0) cc_final: 0.7090 (t0)
REVERT: B   19 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7790 (ttp80)
REVERT: B  118 ASP cc_start: 0.7795 (p0) cc_final: 0.7584 (p0)
REVERT: B  173 THR cc_start: 0.8443 (t) cc_final: 0.8220 (t)
REVERT: B  175 GLN cc_start: 0.8057 (pt0) cc_final: 0.7855 (pt0)
REVERT: B  188 MET cc_start: 0.7871 (mmm) cc_final: 0.7328 (mmm)
REVERT: B  212 ASP cc_start: 0.7584 (p0) cc_final: 0.7105 (p0)
REVERT: B  217 MET cc_start: 0.7847 (pmm) cc_final: 0.7509 (pmm)
REVERT: B  230 ASN cc_start: 0.8236 (m-40) cc_final: 0.7916 (m110)
REVERT: B  246 ASP cc_start: 0.8080 (m-30) cc_final: 0.7652 (m-30)
REVERT: B  258 ASP cc_start: 0.7655 (t0) cc_final: 0.7073 (t0)
REVERT: B  262 MET cc_start: 0.7961 (tpt) cc_final: 0.7511 (mmm)
REVERT: C   20 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.7354 (mpt-90)
REVERT: C   29 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7776 (tp-100)
REVERT: C   31 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7700 (mm-40)
REVERT: C   33 ASP cc_start: 0.7608 (p0) cc_final: 0.7165 (p0)
REVERT: C   60 MET cc_start: 0.4499 (OUTLIER) cc_final: 0.3806 (ttm)
REVERT: C  218 ASN cc_start: 0.7684 (m-40) cc_final: 0.7287 (m-40)
REVERT: C  219 PHE cc_start: 0.8110 (m-10) cc_final: 0.7701 (m-80)
REVERT: C  279 ASN cc_start: 0.8465 (t0) cc_final: 0.8219 (t0)
REVERT: C  289 LEU cc_start: 0.7850 (tp) cc_final: 0.7599 (tp)
REVERT: C  342 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7660 (ttt-90)
REVERT: C  376 PHE cc_start: 0.8192 (t80) cc_final: 0.7729 (t80)
REVERT: C  378 ASP cc_start: 0.7866 (m-30) cc_final: 0.7364 (m-30)
REVERT: D  169 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7316 (mt)
REVERT: D  183 THR cc_start: 0.7257 (t) cc_final: 0.6859 (p)
REVERT: N   38 ARG cc_start: 0.7721 (ptt90) cc_final: 0.7262 (ptt90)
REVERT: N   39 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7957 (tt0)
REVERT: N   65 LYS cc_start: 0.8244 (tptp) cc_final: 0.7993 (tppp)
REVERT: N  120 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7644 (mm-40)
  outliers start: 44
  outliers final: 33
  residues processed: 310
  average time/residue: 0.1079
  time to fit residues: 45.2459
Evaluate side-chains
  325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 286
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  286 SER
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 76 optimal weight:    0.0070
   chunk 119 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 110 ASN
C 236 GLN
C 267 GLN
C 377 ASN
C 384 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.130425 restraints weight = 15062.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.50
r_work: 0.3575 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10266  Z= 0.133
  Angle     :  0.619  11.191  13967  Z= 0.314
  Chirality :  0.042   0.168   1637
  Planarity :  0.004   0.055   1761
  Dihedral  :  4.282  18.516   1415
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 27.72 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.24), residues: 1292
  helix:  2.03 (0.21), residues: 619
  sheet:  0.35 (0.34), residues: 213
  loop : -0.82 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 197 
 TYR   0.010   0.001   TYR A 213 
 PHE   0.020   0.001   PHE D 101 
 TRP   0.015   0.001   TRP C 281 
 HIS   0.009   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10262)
  covalent geometry    : angle       0.61889 (13959)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.39919 (    8)
  hydrogen bonds       : bond        0.04213 (  577)
  hydrogen bonds       : angle       4.21110 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 288
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8542 (mt) cc_final: 0.8297 (mp)
REVERT: A   87 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: A  127 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8013 (mp)
REVERT: A  157 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8305 (mt)
REVERT: A  177 CYS cc_start: 0.5277 (t) cc_final: 0.4988 (t)
REVERT: A  225 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7355 (mp10)
REVERT: B   19 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7664 (ttp80)
REVERT: B  118 ASP cc_start: 0.7780 (p0) cc_final: 0.7570 (p0)
REVERT: B  150 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7815 (mmt-90)
REVERT: B  173 THR cc_start: 0.8413 (t) cc_final: 0.8195 (t)
REVERT: B  175 GLN cc_start: 0.8073 (pt0) cc_final: 0.7865 (pt0)
REVERT: B  188 MET cc_start: 0.7871 (mmm) cc_final: 0.7240 (mmm)
REVERT: B  212 ASP cc_start: 0.7594 (p0) cc_final: 0.7110 (p0)
REVERT: B  217 MET cc_start: 0.7872 (pmm) cc_final: 0.7519 (pmm)
REVERT: B  230 ASN cc_start: 0.8202 (m-40) cc_final: 0.7896 (m110)
REVERT: B  246 ASP cc_start: 0.8039 (m-30) cc_final: 0.7587 (m-30)
REVERT: B  262 MET cc_start: 0.7935 (tpt) cc_final: 0.7468 (mmm)
REVERT: B  273 ILE cc_start: 0.8458 (mp) cc_final: 0.8216 (mt)
REVERT: B  313 ASN cc_start: 0.8685 (t0) cc_final: 0.8275 (t0)
REVERT: C   20 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7357 (mpt-90)
REVERT: C   29 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7778 (tp-100)
REVERT: C   31 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7679 (mm-40)
REVERT: C   33 ASP cc_start: 0.7620 (p0) cc_final: 0.7178 (p0)
REVERT: C   60 MET cc_start: 0.4499 (OUTLIER) cc_final: 0.3850 (ttm)
REVERT: C  218 ASN cc_start: 0.7677 (m-40) cc_final: 0.7296 (m-40)
REVERT: C  219 PHE cc_start: 0.8120 (m-10) cc_final: 0.7719 (m-80)
REVERT: C  279 ASN cc_start: 0.8444 (t0) cc_final: 0.8184 (t0)
REVERT: C  342 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7658 (ttt-90)
REVERT: C  376 PHE cc_start: 0.8166 (t80) cc_final: 0.7731 (t80)
REVERT: C  378 ASP cc_start: 0.7869 (m-30) cc_final: 0.7375 (m-30)
REVERT: D  130 ILE cc_start: 0.8718 (mt) cc_final: 0.8404 (tt)
REVERT: N   65 LYS cc_start: 0.8242 (tptp) cc_final: 0.7994 (tppp)
REVERT: N  120 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7634 (mm-40)
  outliers start: 37
  outliers final: 27
  residues processed: 303
  average time/residue: 0.1099
  time to fit residues: 45.0444
Evaluate side-chains
  321 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 289
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain C residue  381 ASP
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 108 optimal weight:    0.0970
   chunk 32 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 77 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
C 236 GLN
C 377 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.154237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132723 restraints weight = 14985.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.58
r_work: 0.3534 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  10266  Z= 0.143
  Angle     :  0.632  12.018  13967  Z= 0.322
  Chirality :  0.042   0.176   1637
  Planarity :  0.004   0.055   1761
  Dihedral  :  4.296  19.020   1415
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 28.28 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.24), residues: 1292
  helix:  2.04 (0.21), residues: 619
  sheet:  0.37 (0.34), residues: 213
  loop : -0.82 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 197 
 TYR   0.010   0.001   TYR A 213 
 PHE   0.020   0.001   PHE D 101 
 TRP   0.014   0.001   TRP C 281 
 HIS   0.010   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10262)
  covalent geometry    : angle       0.63243 (13959)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       0.34238 (    8)
  hydrogen bonds       : bond        0.04262 (  577)
  hydrogen bonds       : angle       4.21377 ( 1683)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 299
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8131 (tmm) cc_final: 0.7719 (tmm)
REVERT: A   77 LEU cc_start: 0.8533 (mt) cc_final: 0.8294 (mp)
REVERT: A  127 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8009 (mp)
REVERT: A  157 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8301 (mt)
REVERT: A  177 CYS cc_start: 0.5486 (t) cc_final: 0.5204 (t)
REVERT: A  225 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7436 (mp10)
REVERT: B   16 ASN cc_start: 0.7736 (t0) cc_final: 0.7085 (t0)
REVERT: B   19 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7846 (ttp80)
REVERT: B  173 THR cc_start: 0.8381 (t) cc_final: 0.8164 (t)
REVERT: B  188 MET cc_start: 0.7884 (mmm) cc_final: 0.7254 (mmm)
REVERT: B  212 ASP cc_start: 0.7566 (p0) cc_final: 0.7076 (p0)
REVERT: B  217 MET cc_start: 0.7909 (pmm) cc_final: 0.7535 (pmm)
REVERT: B  230 ASN cc_start: 0.8250 (m-40) cc_final: 0.7940 (m110)
REVERT: B  246 ASP cc_start: 0.8039 (m-30) cc_final: 0.7591 (m-30)
REVERT: B  262 MET cc_start: 0.7980 (tpt) cc_final: 0.7501 (mmm)
REVERT: B  273 ILE cc_start: 0.8472 (mp) cc_final: 0.8235 (mt)
REVERT: B  283 ARG cc_start: 0.8251 (tpt170) cc_final: 0.8033 (tpt90)
REVERT: C   20 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7354 (mpt-90)
REVERT: C   29 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7761 (tp-100)
REVERT: C   31 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7699 (mm-40)
REVERT: C   33 ASP cc_start: 0.7559 (p0) cc_final: 0.7110 (p0)
REVERT: C   60 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.3859 (ttm)
REVERT: C  218 ASN cc_start: 0.7678 (m-40) cc_final: 0.7281 (m-40)
REVERT: C  219 PHE cc_start: 0.8112 (m-10) cc_final: 0.7720 (m-80)
REVERT: C  274 ASP cc_start: 0.7984 (t0) cc_final: 0.7737 (t0)
REVERT: C  279 ASN cc_start: 0.8449 (t0) cc_final: 0.8162 (t0)
REVERT: C  307 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7307 (mmtt)
REVERT: C  342 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7629 (ttt-90)
REVERT: C  376 PHE cc_start: 0.8184 (t80) cc_final: 0.7773 (t80)
REVERT: C  378 ASP cc_start: 0.7937 (m-30) cc_final: 0.7440 (m-30)
REVERT: D  130 ILE cc_start: 0.8762 (mt) cc_final: 0.8449 (tt)
REVERT: D  169 LEU cc_start: 0.7592 (mt) cc_final: 0.7269 (mt)
REVERT: D  183 THR cc_start: 0.7227 (t) cc_final: 0.6835 (p)
REVERT: N   39 GLN cc_start: 0.8297 (tt0) cc_final: 0.7982 (tt0)
REVERT: N   65 LYS cc_start: 0.8253 (tptp) cc_final: 0.7983 (tppp)
REVERT: N  120 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7596 (mm-40)
  outliers start: 32
  outliers final: 25
  residues processed: 310
  average time/residue: 0.1101
  time to fit residues: 45.7389
Evaluate side-chains
  326 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 297
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  372 ILE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  177 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 125 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 112 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
C 377 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.153267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.132164 restraints weight = 15019.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.54
r_work: 0.3540 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084  10266  Z= 0.177
  Angle     :  0.659  14.426  13967  Z= 0.336
  Chirality :  0.043   0.176   1637
  Planarity :  0.004   0.056   1761
  Dihedral  :  4.389  19.575   1415
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 28.00 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.24), residues: 1292
  helix:  1.83 (0.21), residues: 631
  sheet:  0.27 (0.34), residues: 219
  loop : -0.81 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 197 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.019   0.002   PHE D 101 
 TRP   0.015   0.002   TRP C 281 
 HIS   0.011   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10262)
  covalent geometry    : angle       0.65931 (13959)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.34351 (    8)
  hydrogen bonds       : bond        0.04483 (  577)
  hydrogen bonds       : angle       4.28664 ( 1683)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2551.91 seconds
wall clock time: 44 minutes 33.74 seconds (2673.74 seconds total)