Starting phenix.real_space_refine
on Wed Sep 17 08:51:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l3y_62798/09_2025/9l3y_62798.cif"
  }
  resolution = 3.6
  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=   0.012 sd=   0.066
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      50      5.16       5
     C    4769      2.51       5
     N    1243      2.21       5
     O    1321      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 7383
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2391
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 10, 'TRANS': 287}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "L"
      Number of atoms: 669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 669
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 225
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "A"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1587
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 65
    Chain: "B"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2408
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 5, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 100
    Chain: "C"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 328
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 34
  Time building chain proxies: 2.13, per 1000 atoms: 0.29
  Number of scatterers: 7383
  At special positions: 0
  Unit cell: (81.396, 95.319, 152.082, 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      50     16.00
     O    1321      8.00
     N    1243      7.00
     C    4769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  77 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  98 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 101 " - pdb=" SG  CYS L 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04

  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: 0.64
  Conformation dependent library (CDL) restraints added in 458.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 9 sheets defined
      38.0% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 36 through 52
      removed outlier: 4.050A  pdb=" N   VAL R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 52 through 63
    Processing helix  chain 'R' and resid 70 through 99
      removed outlier: 3.679A  pdb=" N   LEU R  74 " --> pdb=" O   THR R  70 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 106 through 141
    Processing helix  chain 'R' and resid 150 through 167
    Processing helix  chain 'R' and resid 202 through 215
      removed outlier: 3.803A  pdb=" N   LEU R 206 " --> pdb=" O   ARG R 202 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR R 207 " --> pdb=" O   HIS R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 233
    Processing helix  chain 'R' and resid 234 through 236
      No H-bonds generated for 'chain 'R' and resid 234 through 236'
    Processing helix  chain 'R' and resid 240 through 268
      removed outlier: 3.833A  pdb=" N   TRP R 246 " --> pdb=" O   SER R 242 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   CYS R 258 " --> pdb=" O   ALA R 254 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TRP R 259 " --> pdb=" O   PHE R 255 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
    Processing helix  chain 'R' and resid 284 through 305
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'L' and resid 24 through 40
      removed outlier: 3.701A  pdb=" N   HIS L  40 " --> pdb=" O   GLU L  36 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 134 through 140
      removed outlier: 3.644A  pdb=" N   VAL L 138 " --> pdb=" O   GLN L 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.627A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.456A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.517A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.738A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.552A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.960A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'C' and resid 13 through 24
    Processing helix  chain 'C' and resid 29 through 45
    Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 178
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 190
      removed outlier: 3.825A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.045A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.005A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.439A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.831A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.042A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.616A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.596A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    343 hydrogen bonds defined for protein.
    1014 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: 1.25

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2342
        1.35 -     1.47: 1974
        1.47 -     1.59: 3170
        1.59 -     1.71: 0
        1.71 -     1.83: 65
  Bond restraints: 7551
  Sorted by residual:
  bond pdb=" C   PHE L  60 "
       pdb=" N   PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.01e-02 9.80e+03 6.61e+00
  bond pdb=" C   LYS L  83 "
       pdb=" N   LYS L  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.344 -0.014 1.47e-02 4.63e+03 9.66e-01
  bond pdb=" CA  LYS R 234 "
       pdb=" C   LYS R 234 "
    ideal  model  delta    sigma   weight residual
    1.523  1.536 -0.013 1.34e-02 5.57e+03 9.54e-01
  bond pdb=" C   GLY R 170 "
       pdb=" N   PRO R 171 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.58e-01
  bond pdb=" CB  PRO R 171 "
       pdb=" CG  PRO R 171 "
    ideal  model  delta    sigma   weight residual
    1.492  1.451  0.041 5.00e-02 4.00e+02 6.88e-01
  ... (remaining 7546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 10055
        1.59 -     3.18: 187
        3.18 -     4.77: 41
        4.77 -     6.36: 10
        6.36 -     7.95: 4
  Bond angle restraints: 10297
  Sorted by residual:
  angle pdb=" N   GLY R 170 "
        pdb=" CA  GLY R 170 "
        pdb=" C   GLY R 170 "
      ideal   model   delta    sigma   weight residual
     112.34  118.39   -6.05 2.04e+00 2.40e-01 8.79e+00
  angle pdb=" CA  LYS R  69 "
        pdb=" CB  LYS R  69 "
        pdb=" CG  LYS R  69 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.69e+00
  angle pdb=" C   LYS R 232 "
        pdb=" N   VAL R 233 "
        pdb=" CA  VAL R 233 "
      ideal   model   delta    sigma   weight residual
     121.97  126.11   -4.14 1.80e+00 3.09e-01 5.29e+00
  angle pdb=" CB  LYS L 103 "
        pdb=" CG  LYS L 103 "
        pdb=" CD  LYS L 103 "
      ideal   model   delta    sigma   weight residual
     111.30  116.56   -5.26 2.30e+00 1.89e-01 5.23e+00
  angle pdb=" CA  LEU A 283 "
        pdb=" CB  LEU A 283 "
        pdb=" CG  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     116.30  124.25   -7.95 3.50e+00 8.16e-02 5.16e+00
  ... (remaining 10292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4017
       17.98 -    35.95: 287
       35.95 -    53.93: 57
       53.93 -    71.91: 9
       71.91 -    89.88: 2
  Dihedral angle restraints: 4372
    sinusoidal: 1477
      harmonic: 2895
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.64  -73.64     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CB  CYS L  77 "
           pdb=" SG  CYS L  77 "
           pdb=" SG  CYS L  87 "
           pdb=" CB  CYS L  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.00  -66.00     1      1.00e+01 1.00e-02 5.69e+01
  dihedral pdb=" CA  TYR R 304 "
           pdb=" C   TYR R 304 "
           pdb=" N   VAL R 305 "
           pdb=" CA  VAL R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 779
       0.030 -    0.061: 307
       0.061 -    0.091: 92
       0.091 -    0.122: 42
       0.122 -    0.152: 6
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CB  VAL R 233 "
            pdb=" CA  VAL R 233 "
            pdb=" CG1 VAL R 233 "
            pdb=" CG2 VAL R 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CB  ILE R 168 "
            pdb=" CA  ILE R 168 "
            pdb=" CG1 ILE R 168 "
            pdb=" CG2 ILE R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1285
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 170 "    0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO R 171 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO R 171 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 171 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  62 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   PHE R  62 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE R  62 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR R  63 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 181 "    0.010 2.00e-02 2.50e+03   1.21e-02 2.58e+00
        pdb=" CG  PHE R 181 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 181 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 181 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 181 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 181 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 181 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1282 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 276
        2.72 -     3.26: 7441
        3.26 -     3.81: 11907
        3.81 -     4.35: 14472
        4.35 -     4.90: 24953
  Nonbonded interactions: 59049
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 114 "
            pdb=" OXT SER L 157 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR R 215 "
            pdb=" OG1 THR R 260 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.278 3.040
  ... (remaining 59044 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.440
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
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      :  0.002   0.041   7556  Z= 0.114
  Angle     :  0.572   7.953  10307  Z= 0.304
  Chirality :  0.039   0.152   1226
  Planarity :  0.004   0.082   1285
  Dihedral  : 12.952  89.885   2469
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.27 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.06 (0.28), residues: 963
  helix:  2.31 (0.29), residues: 353
  sheet: -0.38 (0.36), residues: 205
  loop : -1.88 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.016   0.001   TYR R 304 
 PHE   0.028   0.001   PHE R 181 
 TRP   0.017   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 7551)
  covalent geometry    : angle       0.57144 (10297)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       0.64629 (   10)
  hydrogen bonds       : bond        0.10399 (  343)
  hydrogen bonds       : angle       6.07532 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.288 
Fit side-chains
REVERT: R   47 LEU cc_start: 0.7858 (mm) cc_final: 0.7605 (mp)
REVERT: A  298 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: B  325 MET cc_start: 0.6707 (ttm) cc_final: 0.6487 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0939
  time to fit residues: 14.2525
Evaluate side-chains
  97 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
R  38 HIS
R  78 ASN
R 118 GLN
L 134 GLN
A  22 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 259 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.087998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.073568 restraints weight = 21309.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.074214 restraints weight = 16487.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.074935 restraints weight = 12622.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.075142 restraints weight = 10776.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.075296 restraints weight = 10374.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   7556  Z= 0.310
  Angle     :  0.779  10.909  10307  Z= 0.405
  Chirality :  0.048   0.165   1226
  Planarity :  0.005   0.055   1285
  Dihedral  :  4.999  28.604   1038
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.52 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.04 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.52 (0.27), residues: 963
  helix:  1.73 (0.28), residues: 355
  sheet: -0.82 (0.35), residues: 210
  loop : -2.06 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 208 
 TYR   0.051   0.004   TYR B 264 
 PHE   0.026   0.003   PHE R  62 
 TRP   0.019   0.003   TRP B  99 
 HIS   0.011   0.002   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00748 ( 7551)
  covalent geometry    : angle       0.77669 (10297)
  SS BOND              : bond        0.01096 (    5)
  SS BOND              : angle       2.06341 (   10)
  hydrogen bonds       : bond        0.04908 (  343)
  hydrogen bonds       : angle       5.52409 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.5778 (tpm170) cc_final: 0.5567 (tpm170)
  outliers start: 10
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1011
  time to fit residues: 14.2034
Evaluate side-chains
  106 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain A residue  351 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
C  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.089977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.076435 restraints weight = 21014.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.076440 restraints weight = 20050.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.077953 restraints weight = 14307.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.078162 restraints weight = 10410.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.078269 restraints weight = 9344.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7556  Z= 0.135
  Angle     :  0.595  11.105  10307  Z= 0.307
  Chirality :  0.041   0.156   1226
  Planarity :  0.004   0.047   1285
  Dihedral  :  4.412  27.796   1038
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.79 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.91 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.38 (0.28), residues: 963
  helix:  1.91 (0.28), residues: 360
  sheet: -0.75 (0.35), residues: 208
  loop : -2.10 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.018   0.001   TYR B 264 
 PHE   0.021   0.001   PHE R  62 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7551)
  covalent geometry    : angle       0.59339 (10297)
  SS BOND              : bond        0.00633 (    5)
  SS BOND              : angle       1.38195 (   10)
  hydrogen bonds       : bond        0.03670 (  343)
  hydrogen bonds       : angle       4.94418 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.278 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8089 (tt) cc_final: 0.7807 (tt)
REVERT: B  127 LYS cc_start: 0.7308 (ptpt) cc_final: 0.7101 (ptpt)
REVERT: B  134 ARG cc_start: 0.5806 (tpm170) cc_final: 0.5579 (tpm170)
REVERT: B  325 MET cc_start: 0.6868 (ttm) cc_final: 0.6568 (ttm)
  outliers start: 11
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1036
  time to fit residues: 14.9622
Evaluate side-chains
  110 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain B residue   52 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.089890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.075997 restraints weight = 21499.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.076475 restraints weight = 15087.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.077457 restraints weight = 11844.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.077929 restraints weight = 9208.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.078050 restraints weight = 8531.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7556  Z= 0.134
  Angle     :  0.580  11.622  10307  Z= 0.299
  Chirality :  0.041   0.153   1226
  Planarity :  0.004   0.047   1285
  Dihedral  :  4.277  28.809   1038
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.00 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.69 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.36 (0.28), residues: 963
  helix:  2.00 (0.28), residues: 359
  sheet: -0.82 (0.35), residues: 208
  loop : -2.10 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.016   0.001   TYR B 264 
 PHE   0.015   0.001   PHE R  62 
 TRP   0.012   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7551)
  covalent geometry    : angle       0.57836 (10297)
  SS BOND              : bond        0.00574 (    5)
  SS BOND              : angle       1.30471 (   10)
  hydrogen bonds       : bond        0.03515 (  343)
  hydrogen bonds       : angle       4.79107 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: R  212 ILE cc_start: 0.8084 (tt) cc_final: 0.7800 (tt)
REVERT: R  270 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5900 (pp)
REVERT: A  344 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (tp)
REVERT: B  134 ARG cc_start: 0.5826 (tpm170) cc_final: 0.5552 (tpm170)
  outliers start: 16
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1046
  time to fit residues: 14.9933
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   51 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 71 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.089542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.075675 restraints weight = 21410.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.076152 restraints weight = 17658.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.076835 restraints weight = 14334.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.077005 restraints weight = 12647.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.077414 restraints weight = 11083.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7556  Z= 0.132
  Angle     :  0.573  11.698  10307  Z= 0.296
  Chirality :  0.041   0.148   1226
  Planarity :  0.004   0.047   1285
  Dihedral  :  4.255  28.961   1038
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.48 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.83 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.32 (0.28), residues: 963
  helix:  2.05 (0.28), residues: 358
  sheet: -0.84 (0.35), residues: 210
  loop : -2.07 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.013   0.001   PHE A 196 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7551)
  covalent geometry    : angle       0.57147 (10297)
  SS BOND              : bond        0.00609 (    5)
  SS BOND              : angle       1.27228 (   10)
  hydrogen bonds       : bond        0.03449 (  343)
  hydrogen bonds       : angle       4.68727 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.334 
Fit side-chains
REVERT: R  134 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8538 (t0)
REVERT: R  212 ILE cc_start: 0.8076 (tt) cc_final: 0.7780 (tt)
REVERT: R  270 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.6076 (pp)
REVERT: B  127 LYS cc_start: 0.6834 (pttp) cc_final: 0.6382 (ptpt)
REVERT: B  134 ARG cc_start: 0.5908 (tpm170) cc_final: 0.5635 (tpm170)
  outliers start: 20
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1053
  time to fit residues: 15.3841
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  134 ASP
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 34 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.088968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.075675 restraints weight = 21581.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.076658 restraints weight = 17384.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.077513 restraints weight = 13104.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.077601 restraints weight = 10347.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.077957 restraints weight = 9598.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7556  Z= 0.143
  Angle     :  0.584  11.974  10307  Z= 0.303
  Chirality :  0.041   0.144   1226
  Planarity :  0.004   0.066   1285
  Dihedral  :  4.287  28.639   1038
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.10 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.37 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.33 (0.28), residues: 963
  helix:  2.06 (0.28), residues: 357
  sheet: -0.88 (0.35), residues: 211
  loop : -2.05 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 208 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.012   0.001   PHE A 196 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7551)
  covalent geometry    : angle       0.58278 (10297)
  SS BOND              : bond        0.00626 (    5)
  SS BOND              : angle       1.29330 (   10)
  hydrogen bonds       : bond        0.03551 (  343)
  hydrogen bonds       : angle       4.71991 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.241 
Fit side-chains
REVERT: R  134 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (t0)
REVERT: R  212 ILE cc_start: 0.8116 (tt) cc_final: 0.7825 (tt)
REVERT: R  270 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6226 (pp)
REVERT: B  134 ARG cc_start: 0.5914 (tpm170) cc_final: 0.5631 (tpm170)
  outliers start: 24
  outliers final: 18
  residues processed: 111
  average time/residue: 0.1037
  time to fit residues: 15.0807
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  134 ASP
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   51 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 68 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.089931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.077055 restraints weight = 21421.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.077178 restraints weight = 15097.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.077797 restraints weight = 13836.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.078028 restraints weight = 10718.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.078137 restraints weight = 10083.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7556  Z= 0.117
  Angle     :  0.560  11.314  10307  Z= 0.291
  Chirality :  0.040   0.145   1226
  Planarity :  0.004   0.056   1285
  Dihedral  :  4.176  28.913   1038
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.48 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.51 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.28), residues: 963
  helix:  2.15 (0.28), residues: 357
  sheet: -0.73 (0.35), residues: 209
  loop : -2.08 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 208 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.012   0.001   PHE A 196 
 TRP   0.014   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7551)
  covalent geometry    : angle       0.55937 (10297)
  SS BOND              : bond        0.00518 (    5)
  SS BOND              : angle       1.11974 (   10)
  hydrogen bonds       : bond        0.03268 (  343)
  hydrogen bonds       : angle       4.60021 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.284 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8055 (tt) cc_final: 0.7795 (tt)
REVERT: R  270 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6098 (pp)
REVERT: R  305 VAL cc_start: 0.7960 (p) cc_final: 0.7689 (p)
REVERT: B  134 ARG cc_start: 0.5894 (tpm170) cc_final: 0.5609 (tpm170)
  outliers start: 25
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1044
  time to fit residues: 14.9362
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue   40 HIS
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0570
   chunk 46 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 306 GLN
** A 347 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 = 0.3714 r_free = 0.3714 target = 0.090067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.076983 restraints weight = 21621.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.076838 restraints weight = 16022.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.077641 restraints weight = 14053.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.077973 restraints weight = 10863.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.078063 restraints weight = 10048.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7556  Z= 0.115
  Angle     :  0.563  12.553  10307  Z= 0.290
  Chirality :  0.040   0.143   1226
  Planarity :  0.004   0.048   1285
  Dihedral  :  4.133  29.049   1038
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.68 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.06 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.28), residues: 963
  helix:  2.06 (0.29), residues: 361
  sheet: -0.67 (0.36), residues: 197
  loop : -2.02 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 208 
 TYR   0.010   0.001   TYR R  45 
 PHE   0.012   0.001   PHE A 196 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7551)
  covalent geometry    : angle       0.56185 (10297)
  SS BOND              : bond        0.00524 (    5)
  SS BOND              : angle       1.10559 (   10)
  hydrogen bonds       : bond        0.03224 (  343)
  hydrogen bonds       : angle       4.56684 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.307 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8071 (tt) cc_final: 0.7823 (tt)
REVERT: R  270 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6100 (pp)
REVERT: R  305 VAL cc_start: 0.7951 (p) cc_final: 0.7682 (p)
REVERT: B  134 ARG cc_start: 0.5883 (tpm170) cc_final: 0.5597 (tpm170)
  outliers start: 23
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1045
  time to fit residues: 15.1880
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 347 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 = 0.3710 r_free = 0.3710 target = 0.090121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.075308 restraints weight = 21024.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.076799 restraints weight = 15223.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.077465 restraints weight = 10936.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.077473 restraints weight = 9487.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.077623 restraints weight = 9618.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7556  Z= 0.139
  Angle     :  0.584  12.029  10307  Z= 0.302
  Chirality :  0.041   0.141   1226
  Planarity :  0.004   0.046   1285
  Dihedral  :  4.221  28.718   1038
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.89 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.06 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.29 (0.28), residues: 963
  helix:  2.01 (0.28), residues: 361
  sheet: -0.79 (0.36), residues: 199
  loop : -2.00 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 208 
 TYR   0.011   0.001   TYR R  45 
 PHE   0.012   0.001   PHE A 196 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.006   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7551)
  covalent geometry    : angle       0.58323 (10297)
  SS BOND              : bond        0.00632 (    5)
  SS BOND              : angle       1.25190 (   10)
  hydrogen bonds       : bond        0.03459 (  343)
  hydrogen bonds       : angle       4.62762 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.284 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8119 (tt) cc_final: 0.7854 (tt)
REVERT: R  270 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6122 (pp)
REVERT: B  134 ARG cc_start: 0.5926 (tpm170) cc_final: 0.5595 (tpm170)
  outliers start: 24
  outliers final: 22
  residues processed: 105
  average time/residue: 0.1051
  time to fit residues: 14.5208
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.088372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.073228 restraints weight = 21192.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.074550 restraints weight = 16155.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.075436 restraints weight = 11191.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.075597 restraints weight = 9291.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.075665 restraints weight = 8789.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7556  Z= 0.206
  Angle     :  0.652  11.888  10307  Z= 0.338
  Chirality :  0.043   0.145   1226
  Planarity :  0.004   0.047   1285
  Dihedral  :  4.565  28.309   1038
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.62 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.06 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.44 (0.28), residues: 963
  helix:  1.84 (0.28), residues: 359
  sheet: -0.92 (0.36), residues: 199
  loop : -1.99 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 208 
 TYR   0.016   0.002   TYR R  96 
 PHE   0.013   0.002   PHE R  89 
 TRP   0.014   0.002   TRP B  99 
 HIS   0.008   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 7551)
  covalent geometry    : angle       0.65065 (10297)
  SS BOND              : bond        0.00853 (    5)
  SS BOND              : angle       1.57707 (   10)
  hydrogen bonds       : bond        0.04061 (  343)
  hydrogen bonds       : angle       4.87286 ( 1014)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8175 (tt) cc_final: 0.7963 (tt)
REVERT: B  134 ARG cc_start: 0.6062 (tpm170) cc_final: 0.5773 (tpm170)
  outliers start: 24
  outliers final: 22
  residues processed: 107
  average time/residue: 0.1028
  time to fit residues: 14.6170
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:   10.0000
   chunk 78 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 86 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** A 347 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 = 0.3700 r_free = 0.3700 target = 0.089405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.076009 restraints weight = 21481.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.076305 restraints weight = 16425.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.077103 restraints weight = 12615.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.077455 restraints weight = 10472.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.077557 restraints weight = 10171.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7556  Z= 0.123
  Angle     :  0.585  11.846  10307  Z= 0.302
  Chirality :  0.041   0.142   1226
  Planarity :  0.004   0.046   1285
  Dihedral  :  4.312  27.876   1038
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.79 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.19 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.33 (0.28), residues: 963
  helix:  2.04 (0.28), residues: 358
  sheet: -0.80 (0.36), residues: 198
  loop : -2.07 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 208 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.012   0.001   PHE A 196 
 TRP   0.015   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7551)
  covalent geometry    : angle       0.58406 (10297)
  SS BOND              : bond        0.00536 (    5)
  SS BOND              : angle       1.14956 (   10)
  hydrogen bonds       : bond        0.03368 (  343)
  hydrogen bonds       : angle       4.63584 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1333.80 seconds
wall clock time: 23 minutes 52.95 seconds (1432.95 seconds total)