Starting phenix.real_space_refine
on Wed Sep 17 10:35:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y02_38801/09_2025/8y02_38801.cif"
  }
  resolution = 2.61
  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=  -0.001 sd=   0.045
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      65      5.16       5
     C    5225      2.51       5
     N    1375      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 8156
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2002
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 12, 'TRANS': 245}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "A"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1582
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 62
    Chain: "B"
      Number of atoms: 2469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2469
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 319}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "G"
      Number of atoms: 356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 356
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 43}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "S"
      Number of atoms: 1727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1727
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   TRP R 158 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CH2 TRP R 158 " occ=0.50
    residue:
      pdb=" N   PHE R 310 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE R 310 " occ=0.50
  Time building chain proxies: 1.94, per 1000 atoms: 0.24
  Number of scatterers: 8156
  At special positions: 0
  Unit cell: (90.47, 116.2, 115.37, 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      65     16.00
     O    1491      8.00
     N    1375      7.00
     C    5225      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  84 " - pdb=" SG  CYS R 296 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 107 " - pdb=" SG  CYS R 184 " distance=2.02
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.02

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 541.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1986

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      33.6% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 60
      Proline residue:  R  50  - end of helix
      removed outlier: 3.500A  pdb=" N   LEU R  56 " --> pdb=" O   ASN R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 79
    Processing helix  chain 'R' and resid 80 through 87
      removed outlier: 3.529A  pdb=" N   CYS R  84 " --> pdb=" O   GLY R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 93
      removed outlier: 3.553A  pdb=" N   VAL R  93 " --> pdb=" O   PHE R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 111
    Processing helix  chain 'R' and resid 111 through 125
      removed outlier: 3.922A  pdb=" N   ALA R 117 " --> pdb=" O   LEU R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 138
    Processing helix  chain 'R' and resid 146 through 164
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.875A  pdb=" N   PHE R 170 " --> pdb=" O   ILE R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 209
      removed outlier: 3.798A  pdb=" N   TRP R 202 " --> pdb=" O   GLU R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 234
    Processing helix  chain 'R' and resid 237 through 262
      removed outlier: 3.505A  pdb=" N   MET R 250 " --> pdb=" O   GLU R 246 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE R 258 " --> pdb=" O   MET R 254 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 262 through 273
    Processing helix  chain 'R' and resid 288 through 305
      removed outlier: 3.647A  pdb=" N   ALA R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   CYS R 296 " --> pdb=" O   SER R 292 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ILE R 297 " --> pdb=" O   LYS R 293 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
      removed outlier: 3.525A  pdb=" N   PHE R 305 " --> pdb=" O   ILE R 301 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 307 through 315
      removed outlier: 3.652A  pdb=" N   CYS R 313 " --> pdb=" O   GLN R 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.555A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.213A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.712A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 4.421A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.311A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.626A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.437A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.524A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.245A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.904A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.850A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.589A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.771A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.576A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.964A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.964A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.900A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.610A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1050 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: 1.34

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1288
        1.27 -     1.41: 2236
        1.41 -     1.55: 4712
        1.55 -     1.69: 11
        1.69 -     1.83: 91
  Bond restraints: 8338
  Sorted by residual:
  bond pdb=" C   MET S 230 "
       pdb=" O   MET S 230 "
    ideal  model  delta    sigma   weight residual
    1.234  1.129  0.105 1.18e-02 7.18e+03 7.93e+01
  bond pdb=" C   TYR S 228 "
       pdb=" O   TYR S 228 "
    ideal  model  delta    sigma   weight residual
    1.234  1.131  0.103 1.22e-02 6.72e+03 7.12e+01
  bond pdb=" C   TRP S  47 "
       pdb=" O   TRP S  47 "
    ideal  model  delta    sigma   weight residual
    1.234  1.136  0.098 1.27e-02 6.20e+03 5.96e+01
  bond pdb=" C   CYS S 229 "
       pdb=" O   CYS S 229 "
    ideal  model  delta    sigma   weight residual
    1.235  1.151  0.084 1.30e-02 5.92e+03 4.13e+01
  bond pdb=" C   ALA R 295 "
       pdb=" O   ALA R 295 "
    ideal  model  delta    sigma   weight residual
    1.236  1.166  0.070 1.29e-02 6.01e+03 2.92e+01
  ... (remaining 8333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 10344
        2.87 -     5.75: 889
        5.75 -     8.62: 64
        8.62 -    11.50: 9
       11.50 -    14.37: 5
  Bond angle restraints: 11311
  Sorted by residual:
  angle pdb=" N   PHE R  81 "
        pdb=" CA  PHE R  81 "
        pdb=" C   PHE R  81 "
      ideal   model   delta    sigma   weight residual
     113.12  100.94   12.18 1.25e+00 6.40e-01 9.49e+01
  angle pdb=" C   LYS R 138 "
        pdb=" CA  LYS R 138 "
        pdb=" CB  LYS R 138 "
      ideal   model   delta    sigma   weight residual
     110.71  119.67   -8.96 9.40e-01 1.13e+00 9.08e+01
  angle pdb=" N   PRO R 167 "
        pdb=" CA  PRO R 167 "
        pdb=" C   PRO R 167 "
      ideal   model   delta    sigma   weight residual
     110.70  119.89   -9.19 1.22e+00 6.72e-01 5.67e+01
  angle pdb=" N   LEU R 128 "
        pdb=" CA  LEU R 128 "
        pdb=" C   LEU R 128 "
      ideal   model   delta    sigma   weight residual
     111.40  102.69    8.71 1.22e+00 6.72e-01 5.10e+01
  angle pdb=" N   TRP R 188 "
        pdb=" CA  TRP R 188 "
        pdb=" C   TRP R 188 "
      ideal   model   delta    sigma   weight residual
     114.04  105.31    8.73 1.24e+00 6.50e-01 4.96e+01
  ... (remaining 11306 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 4436
       17.27 -    34.54: 300
       34.54 -    51.81: 108
       51.81 -    69.09: 27
       69.09 -    86.36: 5
  Dihedral angle restraints: 4876
    sinusoidal: 1793
      harmonic: 3083
  Sorted by residual:
  dihedral pdb=" CD  ARG B 219 "
           pdb=" NE  ARG B 219 "
           pdb=" CZ  ARG B 219 "
           pdb=" NH1 ARG B 219 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.69  -81.69     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS R  84 "
           pdb=" SG  CYS R  84 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.58  -76.58     1      1.00e+01 1.00e-02 7.37e+01
  dihedral pdb=" CB  CYS S 159 "
           pdb=" SG  CYS S 159 "
           pdb=" SG  CYS S 229 "
           pdb=" CB  CYS S 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.34   60.66     1      1.00e+01 1.00e-02 4.90e+01
  ... (remaining 4873 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 914
       0.108 -    0.216: 296
       0.216 -    0.323: 61
       0.323 -    0.431: 10
       0.431 -    0.539: 2
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" CA  GLN B  75 "
            pdb=" N   GLN B  75 "
            pdb=" C   GLN B  75 "
            pdb=" CB  GLN B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.26e+00
  chirality pdb=" CA  TYR R 298 "
            pdb=" N   TYR R 298 "
            pdb=" C   TYR R 298 "
            pdb=" CB  TYR R 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.09e+00
  chirality pdb=" CA  TYR R 195 "
            pdb=" N   TYR R 195 "
            pdb=" C   TYR R 195 "
            pdb=" CB  TYR R 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.11e+00
  ... (remaining 1280 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "    1.099 9.50e-02 1.11e+02   4.93e-01 1.46e+02
        pdb=" NE  ARG B 219 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET R 401 "   -0.066 2.00e-02 2.50e+03   4.61e-02 2.65e+01
        pdb=" C11 RET R 401 "    0.054 2.00e-02 2.50e+03
        pdb=" C19 RET R 401 "   -0.001 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "    0.047 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.038 2.00e-02 2.50e+03   3.00e-02 1.79e+01
        pdb=" CG  TYR B  59 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 811
        2.73 -     3.27: 7402
        3.27 -     3.81: 13544
        3.81 -     4.36: 17967
        4.36 -     4.90: 29864
  Nonbonded interactions: 69588
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   GLY B 144 "
            pdb=" OG  SER B 161 "
     model   vdw
     2.344 3.040
  ... (remaining 69583 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.240
  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:8.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
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      :  0.016   0.128   8342  Z= 0.917
  Angle     :  1.658  31.535  11317  Z= 1.102
  Chirality :  0.110   0.539   1283
  Planarity :  0.015   0.493   1427
  Dihedral  : 14.403  86.357   2881
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.17 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  :  6.92 %
    Favored  : 84.74 %
  Cbeta Deviations :  1.21 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.34 (0.24), residues: 1045
  helix: -1.64 (0.25), residues: 336
  sheet: -0.81 (0.32), residues: 263
  loop : -1.81 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG B 314 
 TYR   0.072   0.006   TYR B  59 
 PHE   0.037   0.004   PHE B 199 
 TRP   0.034   0.006   TRP B 332 
 HIS   0.020   0.005   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.01620 ( 8338)
  covalent geometry    : angle       1.62128 (11311)
  SS BOND              : bond        0.01103 (    3)
  SS BOND              : angle      15.14654 (    6)
  hydrogen bonds       : bond        0.21172 (  370)
  hydrogen bonds       : angle       8.85548 ( 1050)
  Misc. bond           : bond        0.11767 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 160
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   46 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6220 (tp)
REVERT: R   67 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7637 (mp10)
REVERT: R   88 VAL cc_start: 0.7661 (t) cc_final: 0.7297 (p)
REVERT: R  109 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6560 (tp)
REVERT: R  144 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.5049 (mtt-85)
REVERT: R  176 ILE cc_start: 0.5768 (OUTLIER) cc_final: 0.5460 (pp)
REVERT: R  196 ARG cc_start: 0.4324 (OUTLIER) cc_final: 0.3959 (mtm110)
REVERT: R  235 GLN cc_start: 0.7424 (tp40) cc_final: 0.7197 (mm-40)
REVERT: A   38 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8374 (tt)
REVERT: A  202 THR cc_start: 0.8298 (m) cc_final: 0.8050 (m)
REVERT: A  330 LYS cc_start: 0.8263 (mttp) cc_final: 0.8000 (mmpt)
REVERT: B   19 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6046 (mpt180)
REVERT: B   22 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7048 (ttm110)
REVERT: B   45 MET cc_start: 0.8852 (mtp) cc_final: 0.8639 (mtm)
REVERT: B   46 ARG cc_start: 0.7301 (mpt90) cc_final: 0.6990 (mpt90)
REVERT: B  212 ASP cc_start: 0.8390 (t0) cc_final: 0.8175 (t70)
REVERT: B  217 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7791 (ppp)
  outliers start: 71
  outliers final: 18
  residues processed: 218
  average time/residue: 0.5403
  time to fit residues: 124.9283
Evaluate side-chains
  148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   84 CYS
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  109 LEU
Chi-restraints excluded: chain R residue  144 ARG
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  196 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  239 THR
Chi-restraints excluded: chain R residue  257 SER
Chi-restraints excluded: chain R residue  260 VAL
Chi-restraints excluded: chain R residue  270 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R  52 ASN
R 241 GLN
R 307 ASN
A 256 ASN
B  75 GLN
B  88 ASN
B  91 HIS
B 119 ASN
B 132 ASN
B 220 GLN
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
S  77 ASN
S 142 GLN
S 194 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.157840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.109027 restraints weight = 8906.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.27
r_work: 0.3211 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8342  Z= 0.152
  Angle     :  0.625   8.372  11317  Z= 0.337
  Chirality :  0.045   0.173   1283
  Planarity :  0.005   0.051   1427
  Dihedral  :  7.790  50.225   1203
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.15 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.25), residues: 1045
  helix:  0.07 (0.28), residues: 336
  sheet: -0.63 (0.31), residues: 270
  loop : -1.45 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 129 
 TYR   0.026   0.002   TYR R 298 
 PHE   0.021   0.002   PHE R 145 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8338)
  covalent geometry    : angle       0.62427 (11311)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       1.41934 (    6)
  hydrogen bonds       : bond        0.04467 (  370)
  hydrogen bonds       : angle       5.55713 ( 1050)
  Misc. bond           : bond        0.00035 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.319 
Fit side-chains
REVERT: R   54 MET cc_start: 0.6428 (mtm) cc_final: 0.6218 (mtm)
REVERT: R  107 CYS cc_start: 0.6545 (OUTLIER) cc_final: 0.5923 (t)
REVERT: R  144 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.4687 (mmt180)
REVERT: R  196 ARG cc_start: 0.4392 (OUTLIER) cc_final: 0.3395 (pmt170)
REVERT: R  197 SER cc_start: 0.7699 (p) cc_final: 0.7344 (m)
REVERT: R  236 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7806 (mp0)
REVERT: R  291 PHE cc_start: 0.7190 (m-10) cc_final: 0.6916 (m-80)
REVERT: A   35 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8274 (ptpp)
REVERT: A  306 GLN cc_start: 0.7854 (mm110) cc_final: 0.7146 (mp10)
REVERT: A  330 LYS cc_start: 0.8098 (mttp) cc_final: 0.7458 (mmpt)
REVERT: B   45 MET cc_start: 0.8999 (mtp) cc_final: 0.8786 (mtm)
REVERT: B   46 ARG cc_start: 0.7809 (mpt90) cc_final: 0.7126 (mpt90)
REVERT: B  219 ARG cc_start: 0.7734 (mtm180) cc_final: 0.7207 (mtt-85)
REVERT: B  260 GLU cc_start: 0.7971 (pt0) cc_final: 0.7561 (tt0)
REVERT: S   18 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7299 (tpt170)
REVERT: S  157 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7730 (mm)
  outliers start: 35
  outliers final: 13
  residues processed: 151
  average time/residue: 0.5910
  time to fit residues: 94.3846
Evaluate side-chains
  123 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  144 ARG
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  196 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  239 THR
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 95 optimal weight:    0.0980
   chunk 41 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
A 256 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.155690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106386 restraints weight = 8824.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.27
r_work: 0.3175 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8342  Z= 0.164
  Angle     :  0.590   9.791  11317  Z= 0.314
  Chirality :  0.045   0.153   1283
  Planarity :  0.004   0.047   1427
  Dihedral  :  6.517  51.049   1175
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 15.14 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.62 (0.25), residues: 1045
  helix:  0.73 (0.29), residues: 336
  sheet: -0.42 (0.31), residues: 270
  loop : -1.25 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.027   0.002   TYR R 298 
 PHE   0.023   0.002   PHE R  81 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8338)
  covalent geometry    : angle       0.58703 (11311)
  SS BOND              : bond        0.00388 (    3)
  SS BOND              : angle       2.44930 (    6)
  hydrogen bonds       : bond        0.04193 (  370)
  hydrogen bonds       : angle       5.17612 ( 1050)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.368 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5750 (t)
REVERT: R  144 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.4627 (mmt180)
REVERT: R  196 ARG cc_start: 0.4536 (OUTLIER) cc_final: 0.3671 (pmt170)
REVERT: R  197 SER cc_start: 0.7695 (p) cc_final: 0.7378 (m)
REVERT: R  236 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7898 (mp0)
REVERT: R  291 PHE cc_start: 0.7226 (m-10) cc_final: 0.6988 (m-80)
REVERT: R  306 MET cc_start: 0.7563 (mtt) cc_final: 0.7341 (mtt)
REVERT: A  202 THR cc_start: 0.7940 (m) cc_final: 0.7702 (m)
REVERT: A  305 CYS cc_start: 0.8007 (m) cc_final: 0.7184 (t)
REVERT: A  306 GLN cc_start: 0.7800 (mm110) cc_final: 0.7563 (mp10)
REVERT: A  330 LYS cc_start: 0.8101 (mttp) cc_final: 0.7410 (mmpt)
REVERT: B   45 MET cc_start: 0.9033 (mtp) cc_final: 0.8799 (mtm)
REVERT: B   46 ARG cc_start: 0.7816 (mpt90) cc_final: 0.7350 (mpt90)
REVERT: B  219 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7137 (mtt-85)
REVERT: B  260 GLU cc_start: 0.7984 (pt0) cc_final: 0.7555 (tt0)
REVERT: S  157 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: S  245 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7348 (mp)
  outliers start: 36
  outliers final: 19
  residues processed: 137
  average time/residue: 0.6140
  time to fit residues: 88.9999
Evaluate side-chains
  133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  144 ARG
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  196 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  239 THR
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 87 optimal weight:    0.2980
   chunk 89 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0770
   chunk 99 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
A 256 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.159714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.111172 restraints weight = 8973.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.29
r_work: 0.3256 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8342  Z= 0.099
  Angle     :  0.506   7.542  11317  Z= 0.270
  Chirality :  0.041   0.145   1283
  Planarity :  0.004   0.050   1427
  Dihedral  :  5.961  51.272   1173
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.61 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.26), residues: 1045
  helix:  1.18 (0.29), residues: 339
  sheet: -0.44 (0.29), residues: 272
  loop : -1.08 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.021   0.001   TYR R 298 
 PHE   0.021   0.001   PHE S  68 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8338)
  covalent geometry    : angle       0.50428 (11311)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       2.03913 (    6)
  hydrogen bonds       : bond        0.03399 (  370)
  hydrogen bonds       : angle       4.82365 ( 1050)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.314 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5784 (t)
REVERT: R  144 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.4517 (mmt180)
REVERT: R  194 LYS cc_start: 0.3805 (OUTLIER) cc_final: 0.2482 (tptp)
REVERT: R  236 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7886 (mp0)
REVERT: R  306 MET cc_start: 0.7538 (mtt) cc_final: 0.7314 (mtt)
REVERT: A   29 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7394 (ttmp)
REVERT: A   35 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8405 (mtmt)
REVERT: A  202 THR cc_start: 0.7902 (m) cc_final: 0.7659 (m)
REVERT: A  305 CYS cc_start: 0.8100 (m) cc_final: 0.7349 (t)
REVERT: A  306 GLN cc_start: 0.7893 (mm110) cc_final: 0.7608 (mp10)
REVERT: A  330 LYS cc_start: 0.8098 (mttp) cc_final: 0.7412 (mmpt)
REVERT: B   46 ARG cc_start: 0.7855 (mpt90) cc_final: 0.7359 (mpt90)
REVERT: B  129 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7415 (tpt90)
REVERT: B  219 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7185 (mtt-85)
REVERT: B  260 GLU cc_start: 0.8018 (pt0) cc_final: 0.7637 (tt0)
REVERT: B  262 MET cc_start: 0.8010 (mmm) cc_final: 0.7700 (mtp)
REVERT: S  157 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7697 (mm)
REVERT: S  160 ARG cc_start: 0.7151 (ptp-110) cc_final: 0.6795 (ptm160)
REVERT: S  186 GLN cc_start: 0.8189 (tt0) cc_final: 0.7938 (tt0)
REVERT: S  245 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7498 (mp)
  outliers start: 25
  outliers final: 10
  residues processed: 139
  average time/residue: 0.6332
  time to fit residues: 93.0290
Evaluate side-chains
  130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  144 ARG
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 74 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
B 237 ASN
S   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110363 restraints weight = 8920.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.25
r_work: 0.3228 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8342  Z= 0.114
  Angle     :  0.506   6.978  11317  Z= 0.269
  Chirality :  0.042   0.147   1283
  Planarity :  0.004   0.051   1427
  Dihedral  :  5.342  48.530   1163
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.78 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.10 (0.26), residues: 1045
  helix:  1.39 (0.29), residues: 340
  sheet: -0.38 (0.29), residues: 269
  loop : -0.98 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.015   0.001   PHE S  68 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8338)
  covalent geometry    : angle       0.50498 (11311)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       1.73290 (    6)
  hydrogen bonds       : bond        0.03447 (  370)
  hydrogen bonds       : angle       4.72599 ( 1050)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.238 
Fit side-chains
REVERT: R   66 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7437 (mtm-85)
REVERT: R  107 CYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5631 (t)
REVERT: R  144 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.4477 (mmt180)
REVERT: R  194 LYS cc_start: 0.3563 (OUTLIER) cc_final: 0.1990 (tmtt)
REVERT: R  236 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7975 (mp0)
REVERT: A   29 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7414 (ttmp)
REVERT: A  202 THR cc_start: 0.7838 (m) cc_final: 0.7592 (m)
REVERT: A  305 CYS cc_start: 0.8090 (m) cc_final: 0.7429 (t)
REVERT: A  306 GLN cc_start: 0.7853 (mm110) cc_final: 0.7576 (mp10)
REVERT: A  330 LYS cc_start: 0.8032 (mttp) cc_final: 0.7360 (mmpt)
REVERT: B   46 ARG cc_start: 0.7867 (mpt90) cc_final: 0.7366 (mpt90)
REVERT: B  129 ARG cc_start: 0.7690 (ttt90) cc_final: 0.7455 (tpt90)
REVERT: B  134 ARG cc_start: 0.8216 (ptp90) cc_final: 0.7751 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7201 (mtt-85)
REVERT: B  260 GLU cc_start: 0.8013 (pt0) cc_final: 0.7589 (tt0)
REVERT: S  160 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6852 (ptm160)
REVERT: S  245 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7415 (mp)
  outliers start: 31
  outliers final: 15
  residues processed: 136
  average time/residue: 0.6328
  time to fit residues: 91.0091
Evaluate side-chains
  131 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  144 ARG
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.157983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108990 restraints weight = 8905.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.27
r_work: 0.3222 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8342  Z= 0.117
  Angle     :  0.507   7.258  11317  Z= 0.269
  Chirality :  0.042   0.144   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  5.312  48.487   1163
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.37 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.10 (0.26), residues: 1045
  helix:  1.67 (0.29), residues: 333
  sheet: -0.37 (0.29), residues: 269
  loop : -0.85 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.013   0.001   PHE S  68 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8338)
  covalent geometry    : angle       0.50541 (11311)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       1.91499 (    6)
  hydrogen bonds       : bond        0.03422 (  370)
  hydrogen bonds       : angle       4.67448 ( 1050)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.331 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5555 (t)
REVERT: R  194 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.2059 (tmtt)
REVERT: R  236 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7945 (mp0)
REVERT: A   29 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7398 (ttmp)
REVERT: A  305 CYS cc_start: 0.8128 (m) cc_final: 0.7502 (t)
REVERT: A  306 GLN cc_start: 0.7851 (mm110) cc_final: 0.7554 (mp10)
REVERT: A  330 LYS cc_start: 0.8031 (mttp) cc_final: 0.7362 (mmpt)
REVERT: B   46 ARG cc_start: 0.7830 (mpt90) cc_final: 0.7357 (mpt90)
REVERT: B  129 ARG cc_start: 0.7751 (ttt90) cc_final: 0.7522 (tpt90)
REVERT: B  134 ARG cc_start: 0.8270 (ptp90) cc_final: 0.7799 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7218 (mtt-85)
REVERT: B  226 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8022 (mm-30)
REVERT: B  260 GLU cc_start: 0.7961 (pt0) cc_final: 0.7641 (tt0)
REVERT: G   47 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7845 (mt-10)
REVERT: S  160 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6845 (ptm160)
REVERT: S  186 GLN cc_start: 0.8216 (tt0) cc_final: 0.8009 (tt0)
REVERT: S  245 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7544 (mp)
  outliers start: 29
  outliers final: 17
  residues processed: 137
  average time/residue: 0.6046
  time to fit residues: 87.8489
Evaluate side-chains
  136 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0070
   chunk 81 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.158120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.109014 restraints weight = 8900.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.27
r_work: 0.3221 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8342  Z= 0.115
  Angle     :  0.502   7.001  11317  Z= 0.266
  Chirality :  0.042   0.144   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  5.099  48.453   1159
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.78 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.27 (0.26), residues: 1045
  helix:  1.86 (0.29), residues: 333
  sheet: -0.27 (0.29), residues: 266
  loop : -0.79 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 144 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.011   0.001   PHE R 145 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8338)
  covalent geometry    : angle       0.49939 (11311)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       2.18002 (    6)
  hydrogen bonds       : bond        0.03356 (  370)
  hydrogen bonds       : angle       4.61738 ( 1050)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.317 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5454 (t)
REVERT: R  194 LYS cc_start: 0.3325 (OUTLIER) cc_final: 0.1931 (tmtt)
REVERT: R  236 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (mp0)
REVERT: A   29 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7423 (ttmp)
REVERT: A  305 CYS cc_start: 0.8061 (m) cc_final: 0.7493 (t)
REVERT: A  306 GLN cc_start: 0.7720 (mm110) cc_final: 0.7414 (mp10)
REVERT: A  330 LYS cc_start: 0.8028 (mttp) cc_final: 0.7351 (mmpt)
REVERT: B   46 ARG cc_start: 0.7819 (mpt90) cc_final: 0.7343 (mpt90)
REVERT: B  129 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7411 (tpt170)
REVERT: B  134 ARG cc_start: 0.8270 (ptp90) cc_final: 0.7794 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7224 (mtt-85)
REVERT: B  226 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7960 (mm-30)
REVERT: B  260 GLU cc_start: 0.7993 (pt0) cc_final: 0.7592 (tt0)
REVERT: S  160 ARG cc_start: 0.7192 (ptp-110) cc_final: 0.6850 (ptm160)
REVERT: S  186 GLN cc_start: 0.8227 (tt0) cc_final: 0.8026 (tt0)
REVERT: S  245 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7542 (mp)
  outliers start: 28
  outliers final: 16
  residues processed: 136
  average time/residue: 0.5631
  time to fit residues: 81.2035
Evaluate side-chains
  135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0570
   chunk 82 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 13 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0670
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110701 restraints weight = 8822.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.27
r_work: 0.3241 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8342  Z= 0.100
  Angle     :  0.493   8.022  11317  Z= 0.262
  Chirality :  0.041   0.160   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  5.004  48.540   1159
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.13 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.40 (0.26), residues: 1045
  helix:  1.99 (0.29), residues: 333
  sheet: -0.20 (0.29), residues: 265
  loop : -0.73 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 144 
 TYR   0.018   0.001   TYR R 298 
 PHE   0.011   0.001   PHE R 205 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 8338)
  covalent geometry    : angle       0.49084 (11311)
  SS BOND              : bond        0.00174 (    3)
  SS BOND              : angle       2.01573 (    6)
  hydrogen bonds       : bond        0.03205 (  370)
  hydrogen bonds       : angle       4.54874 ( 1050)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.330 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6099 (t)
REVERT: R  194 LYS cc_start: 0.3198 (OUTLIER) cc_final: 0.1808 (tmtt)
REVERT: R  236 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7966 (mp0)
REVERT: A   29 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7442 (ttmp)
REVERT: A  306 GLN cc_start: 0.7679 (mm110) cc_final: 0.7382 (mp10)
REVERT: A  330 LYS cc_start: 0.8017 (mttp) cc_final: 0.7326 (mmpt)
REVERT: B   46 ARG cc_start: 0.7827 (mpt90) cc_final: 0.7351 (mpt90)
REVERT: B  129 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7357 (tpt170)
REVERT: B  134 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7781 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7204 (mtt-85)
REVERT: B  260 GLU cc_start: 0.8046 (pt0) cc_final: 0.7677 (tt0)
REVERT: B  262 MET cc_start: 0.8036 (mtp) cc_final: 0.7705 (mtp)
REVERT: S  113 GLN cc_start: 0.8034 (mm110) cc_final: 0.7804 (mm-40)
REVERT: S  118 THR cc_start: 0.7678 (p) cc_final: 0.7420 (t)
REVERT: S  160 ARG cc_start: 0.7206 (ptp-110) cc_final: 0.6873 (ptm160)
REVERT: S  186 GLN cc_start: 0.8268 (tt0) cc_final: 0.7720 (pt0)
REVERT: S  245 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7562 (mp)
  outliers start: 29
  outliers final: 16
  residues processed: 137
  average time/residue: 0.6096
  time to fit residues: 88.3903
Evaluate side-chains
  135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
B 237 ASN
S   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.157802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.108737 restraints weight = 8831.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.25
r_work: 0.3219 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8342  Z= 0.124
  Angle     :  0.516   8.785  11317  Z= 0.272
  Chirality :  0.042   0.168   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  5.086  48.689   1159
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.72 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.40 (0.26), residues: 1045
  helix:  2.01 (0.29), residues: 333
  sheet: -0.21 (0.29), residues: 261
  loop : -0.72 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 144 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.013   0.001   PHE S 212 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8338)
  covalent geometry    : angle       0.51380 (11311)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       2.04661 (    6)
  hydrogen bonds       : bond        0.03373 (  370)
  hydrogen bonds       : angle       4.57384 ( 1050)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.320 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6144 (t)
REVERT: R  194 LYS cc_start: 0.3136 (OUTLIER) cc_final: 0.1777 (tmtt)
REVERT: R  236 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7979 (mp0)
REVERT: A  305 CYS cc_start: 0.8159 (m) cc_final: 0.7595 (t)
REVERT: A  306 GLN cc_start: 0.7715 (mm110) cc_final: 0.7458 (mp10)
REVERT: A  330 LYS cc_start: 0.8046 (mttp) cc_final: 0.7373 (mmpt)
REVERT: B   46 ARG cc_start: 0.7829 (mpt90) cc_final: 0.7356 (mpt90)
REVERT: B  134 ARG cc_start: 0.8272 (ptp90) cc_final: 0.7807 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7269 (mtt-85)
REVERT: B  226 GLU cc_start: 0.8509 (mp0) cc_final: 0.8235 (mm-30)
REVERT: B  260 GLU cc_start: 0.8036 (pt0) cc_final: 0.7673 (tt0)
REVERT: B  262 MET cc_start: 0.8035 (mtp) cc_final: 0.7730 (mtp)
REVERT: G   47 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7865 (mt-10)
REVERT: S  113 GLN cc_start: 0.8107 (mm110) cc_final: 0.7887 (mm-40)
REVERT: S  160 ARG cc_start: 0.7229 (ptp-110) cc_final: 0.6911 (ptm160)
REVERT: S  186 GLN cc_start: 0.8284 (tt0) cc_final: 0.7765 (pt0)
REVERT: S  245 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7557 (mp)
  outliers start: 25
  outliers final: 17
  residues processed: 130
  average time/residue: 0.6179
  time to fit residues: 84.9986
Evaluate side-chains
  133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 15 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0970
   chunk 102 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
R 241 GLN
A 322 HIS
S   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.160212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.111808 restraints weight = 8882.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.26
r_work: 0.3257 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8342  Z= 0.094
  Angle     :  0.481   9.103  11317  Z= 0.253
  Chirality :  0.041   0.144   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  4.936  48.674   1159
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.31 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.53 (0.26), residues: 1045
  helix:  2.13 (0.29), residues: 333
  sheet: -0.14 (0.29), residues: 265
  loop : -0.68 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 144 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.013   0.001   PHE S 212 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8338)
  covalent geometry    : angle       0.47942 (11311)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.77902 (    6)
  hydrogen bonds       : bond        0.03087 (  370)
  hydrogen bonds       : angle       4.45014 ( 1050)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.289 
Fit side-chains
REVERT: R  107 CYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6197 (t)
REVERT: R  194 LYS cc_start: 0.2958 (OUTLIER) cc_final: 0.1766 (tmtt)
REVERT: R  236 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7983 (mp0)
REVERT: A  306 GLN cc_start: 0.7674 (mm110) cc_final: 0.7433 (mp10)
REVERT: A  329 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6509 (p)
REVERT: A  330 LYS cc_start: 0.8025 (mttp) cc_final: 0.7333 (mmpt)
REVERT: B   46 ARG cc_start: 0.7834 (mpt90) cc_final: 0.7392 (mpt90)
REVERT: B  134 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7821 (ppt-90)
REVERT: B  219 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7229 (mtt-85)
REVERT: B  226 GLU cc_start: 0.8492 (mp0) cc_final: 0.8220 (mm-30)
REVERT: B  260 GLU cc_start: 0.8033 (pt0) cc_final: 0.7669 (tt0)
REVERT: B  262 MET cc_start: 0.7990 (mtp) cc_final: 0.7757 (mtp)
REVERT: G   47 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7856 (mt-10)
REVERT: S  160 ARG cc_start: 0.7202 (ptp-110) cc_final: 0.6860 (mtp-110)
REVERT: S  186 GLN cc_start: 0.8245 (tt0) cc_final: 0.7754 (pt0)
REVERT: S  245 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7546 (mp)
  outliers start: 21
  outliers final: 14
  residues processed: 130
  average time/residue: 0.5714
  time to fit residues: 78.7993
Evaluate side-chains
  131 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  190 THR
Chi-restraints excluded: chain R residue  194 LYS
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  236 GLU
Chi-restraints excluded: chain R residue  265 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
R 233 GLN
R 235 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.156147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106650 restraints weight = 8877.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.26
r_work: 0.3195 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8342  Z= 0.162
  Angle     :  0.548   9.006  11317  Z= 0.288
  Chirality :  0.044   0.169   1283
  Planarity :  0.004   0.052   1427
  Dihedral  :  5.214  48.825   1159
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 20.07 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.42 (0.26), residues: 1045
  helix:  2.05 (0.29), residues: 333
  sheet: -0.15 (0.29), residues: 262
  loop : -0.77 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 144 
 TYR   0.019   0.001   TYR R 298 
 PHE   0.028   0.002   PHE S  68 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8338)
  covalent geometry    : angle       0.54248 (11311)
  SS BOND              : bond        0.00285 (    3)
  SS BOND              : angle       3.30038 (    6)
  hydrogen bonds       : bond        0.03595 (  370)
  hydrogen bonds       : angle       4.64478 ( 1050)
  Misc. bond           : bond        0.00017 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4320.18 seconds
wall clock time: 74 minutes 11.39 seconds (4451.39 seconds total)