Starting phenix.real_space_refine
on Fri Oct 23 15:33:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ycx_72790/10_2026/9ycx_72790.map"
  }
  resolution = 2.1
  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=  -0.000 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2034 atoms to isotropic.
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      58      5.16       5
     C    5481      2.51       5
     N    1462      2.21       5
     O    1566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8567
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2505
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 70
    Chain: "C"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 384
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 29
    Chain: "L"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 60
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2273
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 292}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 76
    Chain: "A"
      Number of atoms: 1638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1638
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 152
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "S"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1707
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
  Time building chain proxies: 2.02, per 1000 atoms: 0.24
  Number of scatterers: 8567
  At special positions: 0
  Unit cell: (93.184, 118.976, 128.96, 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      58     16.00
     O    1566      8.00
     N    1462      7.00
     C    5481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 321.8 milliseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      39.5% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.743A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.624A  pdb=" N   ASP R  55 " --> pdb=" O   SER R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 91
    Processing helix  chain 'R' and resid 99 through 126
      removed outlier: 3.688A  pdb=" N   ALA R 119 " --> pdb=" O   THR R 115 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 136 through 172
    Processing helix  chain 'R' and resid 175 through 180
    Processing helix  chain 'R' and resid 181 through 201
    Processing helix  chain 'R' and resid 201 through 206
      removed outlier: 4.224A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 272
    Processing helix  chain 'R' and resid 293 through 329
      removed outlier: 3.717A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.872A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 334
    Processing helix  chain 'R' and resid 335 through 366
      removed outlier: 3.628A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASN R 360 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 3.724A  pdb=" N   TYR R 364 " --> pdb=" O   ASN R 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.836A  pdb=" N   LYS A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.463A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.142A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.748A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ARG A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.557A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.251A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.650A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.815A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.957A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.704A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.896A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.717A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.753A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 207 through 211
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.279A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.845A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.382A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.546A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.546A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1341 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: 1.32

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2772
        1.34 -     1.47: 2236
        1.47 -     1.59: 3661
        1.59 -     1.71: 0
        1.71 -     1.83: 86
  Bond restraints: 8755
  Sorted by residual:
  bond pdb=" CB  ASN B 340 "
       pdb=" CG  ASN B 340 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.97e-01
  bond pdb=" CA  GLY B 319 "
       pdb=" C   GLY B 319 "
    ideal  model  delta    sigma   weight residual
    1.509  1.518 -0.009 9.20e-03 1.18e+04 9.25e-01
  bond pdb=" CG  PRO R 361 "
       pdb=" CD  PRO R 361 "
    ideal  model  delta    sigma   weight residual
    1.503  1.471  0.032 3.40e-02 8.65e+02 8.87e-01
  bond pdb=" CB  PRO R 361 "
       pdb=" CG  PRO R 361 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 6.13e-01
  bond pdb=" CB  VAL R 267 "
       pdb=" CG2 VAL R 267 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.85e-01
  ... (remaining 8750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11734
        1.73 -     3.46: 172
        3.46 -     5.19: 19
        5.19 -     6.92: 5
        6.92 -     8.65: 1
  Bond angle restraints: 11931
  Sorted by residual:
  angle pdb=" N   GLY B 319 "
        pdb=" CA  GLY B 319 "
        pdb=" C   GLY B 319 "
      ideal   model   delta    sigma   weight residual
     110.87  116.33   -5.46 1.54e+00 4.22e-01 1.26e+01
  angle pdb=" CA  TRP B  82 "
        pdb=" CB  TRP B  82 "
        pdb=" CG  TRP B  82 "
      ideal   model   delta    sigma   weight residual
     113.60  119.02   -5.42 1.90e+00 2.77e-01 8.13e+00
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     121.54  126.70   -5.16 1.91e+00 2.74e-01 7.29e+00
  angle pdb=" CA  LEU B 318 "
        pdb=" CB  LEU B 318 "
        pdb=" CG  LEU B 318 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  angle pdb=" CA  PRO R 361 "
        pdb=" N   PRO R 361 "
        pdb=" CD  PRO R 361 "
      ideal   model   delta    sigma   weight residual
     112.00  108.63    3.37 1.40e+00 5.10e-01 5.80e+00
  ... (remaining 11926 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4644
       17.98 -    35.97: 336
       35.97 -    53.95: 86
       53.95 -    71.93: 23
       71.93 -    89.91: 9
  Dihedral angle restraints: 5098
    sinusoidal: 1744
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.72   43.28     1      1.00e+01 1.00e-02 2.61e+01
  dihedral pdb=" CA  ILE R 359 "
           pdb=" C   ILE R 359 "
           pdb=" N   ASN R 360 "
           pdb=" CA  ASN R 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 5095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 847
       0.032 -    0.063: 360
       0.063 -    0.095: 120
       0.095 -    0.127: 56
       0.127 -    0.158: 9
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CA  VAL S  37 "
            pdb=" N   VAL S  37 "
            pdb=" C   VAL S  37 "
            pdb=" CB  VAL S  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1389 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 360 "    0.053 5.00e-02 4.00e+02   7.91e-02 1.00e+01
        pdb=" N   PRO R 361 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO R 361 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 361 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.032 5.00e-02 4.00e+02   4.79e-02 3.67e+00
        pdb=" N   PRO B 236 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 205 "    0.008 2.00e-02 2.50e+03   1.09e-02 2.07e+00
        pdb=" CG  PHE R 205 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 205 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 205 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 205 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 205 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 205 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3291
        2.89 -     3.39: 7973
        3.39 -     3.90: 14694
        3.90 -     4.40: 16373
        4.40 -     4.90: 28330
  Nonbonded interactions: 70661
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" O   ASP S  74 "
            pdb=" ND2 ASN S  77 "
     model   vdw
     2.392 3.120
  nonbonded pdb=" NH1 ARG L   9 "
            pdb=" O   PHE R 326 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.410 3.040
  nonbonded pdb=" NH1 ARG R 142 "
            pdb=" O   LEU R 204 "
     model   vdw
     2.411 3.120
  ... (remaining 70656 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.270
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:5.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8757  Z= 0.147
  Angle     :  0.559   8.651  11935  Z= 0.311
  Chirality :  0.043   0.158   1392
  Planarity :  0.004   0.079   1511
  Dihedral  : 14.847  89.914   2928
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.59 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.89 (0.25), residues: 1132
  helix:  2.97 (0.24), residues: 398
  sheet:  0.96 (0.30), residues: 294
  loop : -0.15 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 166 
 TYR   0.018   0.002   TYR R 125 
 PHE   0.025   0.002   PHE R 205 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.15 ( 8755)
  covalent geometry    : angle       0.55786 /  0.31 (11931)
  SS BOND              : bond        0.01047 /  0.50 (    2)
  SS BOND              : angle       2.16510 /  1.01 (    4)
  hydrogen bonds       : bond        0.11281 /  8.20 (  472)
  hydrogen bonds       : angle       5.31392 /  3.68 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  284 THR cc_start: 0.7553 (m) cc_final: 0.7297 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 134
  average time/residue: 0.6101
  time to fit residues: 86.5743
Evaluate side-chains
  133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  330 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106]
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    3.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
R 158 ASN
R 320 HIS
R 350 ASN
A 347 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.178763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.121502 restraints weight = 7640.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.66
r_work: 0.3188 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.0800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8757  Z= 0.257
  Angle     :  0.712  11.223  11935  Z= 0.394
  Chirality :  0.049   0.179   1392
  Planarity :  0.006   0.059   1511
  Dihedral  :  5.284  44.830   1243
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.32 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.53 (0.24), residues: 1132
  helix:  2.58 (0.24), residues: 389
  sheet:  0.75 (0.30), residues: 294
  loop : -0.17 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 166 
 TYR   0.026   0.003   TYR S 103 
 PHE   0.027   0.003   PHE A 215 
 TRP   0.022   0.003   TRP B  82 
 HIS   0.007   0.002   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.26 ( 8755)
  covalent geometry    : angle       0.71105 /  0.39 (11931)
  SS BOND              : bond        0.01439 /  0.69 (    2)
  SS BOND              : angle       2.46997 /  1.13 (    4)
  hydrogen bonds       : bond        0.06815 /  4.78 (  472)
  hydrogen bonds       : angle       5.02588 /  3.51 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.218 
Fit side-chains
REVERT: B  226 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8526 (mp0)
REVERT: L    9 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6194 (ttm-80)
REVERT: A   28 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6808 (mp0)
REVERT: A  284 THR cc_start: 0.7726 (m) cc_final: 0.7489 (p)
  outliers start: 25
  outliers final: 8
  residues processed: 151
  average time/residue: 0.6243
  time to fit residues: 99.6461
Evaluate side-chains
  144 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain L residue    9 ARG
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [36, 21, 58, 84, 54, 96, 24, 83, 94, 31, 11]
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 54 optimal weight:   50.0000
   chunk 96 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 94 optimal weight:    0.0370
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6460

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  32 GLN
B 266 HIS
R 158 ASN
R 350 ASN
A 331 ASN
A 347 ASN
S  77 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.181829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.121330 restraints weight = 7735.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.72
r_work: 0.3185 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8757  Z= 0.107
  Angle     :  0.486   7.329  11935  Z= 0.271
  Chirality :  0.041   0.138   1392
  Planarity :  0.004   0.048   1511
  Dihedral  :  4.492  39.698   1240
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.40 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.90 (0.25), residues: 1132
  helix:  3.05 (0.24), residues: 398
  sheet:  0.89 (0.30), residues: 287
  loop : -0.12 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 142 
 TYR   0.016   0.001   TYR S 178 
 PHE   0.012   0.001   PHE R 353 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.003   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00198 /  0.11 ( 8755)
  covalent geometry    : angle       0.48476 /  0.27 (11931)
  SS BOND              : bond        0.00636 /  0.30 (    2)
  SS BOND              : angle       1.69101 /  0.80 (    4)
  hydrogen bonds       : bond        0.04468 /  3.13 (  472)
  hydrogen bonds       : angle       4.43606 /  3.08 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B  217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7973 (pmt)
REVERT: B  226 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8519 (mp0)
REVERT: S  211 ASP cc_start: 0.8557 (m-30) cc_final: 0.8343 (m-30)
  outliers start: 19
  outliers final: 6
  residues processed: 139
  average time/residue: 0.5952
  time to fit residues: 87.8776
Evaluate side-chains
  136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [31, 96, 91, 101, 61, 102, 44, 11, 111, 78, 41]
   chunk 31 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 102 optimal weight:    0.3980
   chunk 44 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  32 GLN
B 266 HIS
C  18 GLN
R 158 ASN
R 350 ASN
A 347 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.180520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118195 restraints weight = 7713.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.67
r_work: 0.3163 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.0871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8757  Z= 0.130
  Angle     :  0.530   8.310  11935  Z= 0.293
  Chirality :  0.042   0.149   1392
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.459  21.758   1237
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.99 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.91 (0.25), residues: 1132
  helix:  3.05 (0.24), residues: 398
  sheet:  0.80 (0.29), residues: 295
  loop : -0.06 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 182 
 TYR   0.016   0.001   TYR S 178 
 PHE   0.017   0.001   PHE A 215 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.13 ( 8755)
  covalent geometry    : angle       0.52873 /  0.29 (11931)
  SS BOND              : bond        0.00882 /  0.42 (    2)
  SS BOND              : angle       1.78896 /  0.85 (    4)
  hydrogen bonds       : bond        0.04918 /  3.44 (  472)
  hydrogen bonds       : angle       4.49833 /  3.12 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.341 
Fit side-chains
REVERT: B   38 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8409 (m-30)
REVERT: B  226 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8469 (mp0)
REVERT: S  211 ASP cc_start: 0.8601 (m-30) cc_final: 0.8367 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 137
  average time/residue: 0.5768
  time to fit residues: 83.9652
Evaluate side-chains
  145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [45, 42, 12, 38, 93, 56, 34, 110, 29, 98, 81]
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0030
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    1.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 158 ASN
R 350 ASN
A 347 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.179216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117463 restraints weight = 7636.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.65
r_work: 0.3141 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8757  Z= 0.167
  Angle     :  0.590   9.089  11935  Z= 0.326
  Chirality :  0.044   0.159   1392
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.696  21.990   1237
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.92 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.81 (0.25), residues: 1132
  helix:  3.01 (0.24), residues: 390
  sheet:  0.76 (0.29), residues: 295
  loop : -0.11 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 182 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.020   0.002   PHE A 215 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.17 ( 8755)
  covalent geometry    : angle       0.58859 /  0.33 (11931)
  SS BOND              : bond        0.01088 /  0.52 (    2)
  SS BOND              : angle       2.17078 /  1.03 (    4)
  hydrogen bonds       : bond        0.05553 /  3.89 (  472)
  hydrogen bonds       : angle       4.65943 /  3.24 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B  226 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (mp0)
REVERT: A  284 THR cc_start: 0.7740 (m) cc_final: 0.7495 (p)
  outliers start: 26
  outliers final: 15
  residues processed: 142
  average time/residue: 0.5753
  time to fit residues: 86.8563
Evaluate side-chains
  147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [23, 48, 108, 25, 80, 102, 16, 64, 1, 103, 55]
   chunk 23 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.0164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 158 ASN
R 350 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.120447 restraints weight = 7595.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.84
r_work: 0.3131 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8757  Z= 0.168
  Angle     :  0.591   9.068  11935  Z= 0.326
  Chirality :  0.044   0.159   1392
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.717  22.246   1237
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.80 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.75 (0.25), residues: 1132
  helix:  2.92 (0.24), residues: 390
  sheet:  0.73 (0.30), residues: 295
  loop : -0.11 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 182 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.020   0.002   PHE R 205 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.17 ( 8755)
  covalent geometry    : angle       0.58954 /  0.33 (11931)
  SS BOND              : bond        0.01035 /  0.50 (    2)
  SS BOND              : angle       2.11784 /  0.99 (    4)
  hydrogen bonds       : bond        0.05539 /  3.88 (  472)
  hydrogen bonds       : angle       4.65713 /  3.24 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.296 
Fit side-chains
REVERT: B  226 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8528 (mp0)
REVERT: A  284 THR cc_start: 0.7713 (m) cc_final: 0.7473 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 146
  average time/residue: 0.5597
  time to fit residues: 87.0789
Evaluate side-chains
  149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain R residue  374 ILE
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [63, 71, 45, 98, 65, 20, 1, 53, 40, 61, 90]
   chunk 63 optimal weight:    5.9990
   chunk 71 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   overall best weight:    2.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 126 ASN
R 158 ASN
R 350 ASN
A 331 ASN
A 347 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.178316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116121 restraints weight = 7661.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.64
r_work: 0.3130 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8757  Z= 0.195
  Angle     :  0.634   9.751  11935  Z= 0.349
  Chirality :  0.046   0.165   1392
  Planarity :  0.004   0.053   1511
  Dihedral  :  4.869  22.297   1237
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.92 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.62 (0.25), residues: 1132
  helix:  2.78 (0.24), residues: 389
  sheet:  0.67 (0.30), residues: 295
  loop : -0.16 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 166 
 TYR   0.021   0.002   TYR S 103 
 PHE   0.023   0.002   PHE R 205 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.19 ( 8755)
  covalent geometry    : angle       0.63309 /  0.35 (11931)
  SS BOND              : bond        0.01203 /  0.58 (    2)
  SS BOND              : angle       2.30917 /  1.06 (    4)
  hydrogen bonds       : bond        0.05959 /  4.18 (  472)
  hydrogen bonds       : angle       4.75756 /  3.32 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B  217 MET cc_start: 0.8606 (pmm) cc_final: 0.8353 (ppp)
REVERT: B  226 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (mp0)
REVERT: R  207 MET cc_start: 0.6790 (mmm) cc_final: 0.6478 (mmm)
REVERT: R  212 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.5180 (mtm180)
REVERT: A  284 THR cc_start: 0.7760 (m) cc_final: 0.7513 (p)
  outliers start: 25
  outliers final: 19
  residues processed: 145
  average time/residue: 0.5775
  time to fit residues: 88.9452
Evaluate side-chains
  150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  212 ARG
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  237 ILE
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain R residue  374 ILE
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [101, 76, 85, 48, 30, 53, 75, 107, 104, 67, 94]
   chunk 101 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 104 optimal weight:    0.2980
   chunk 67 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 126 ASN
R 158 ASN
R 350 ASN
A 347 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.178885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.118460 restraints weight = 7608.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.67
r_work: 0.3130 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8757  Z= 0.169
  Angle     :  0.597   9.130  11935  Z= 0.329
  Chirality :  0.045   0.194   1392
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.781  22.653   1237
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.28 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.67 (0.25), residues: 1132
  helix:  2.85 (0.24), residues: 390
  sheet:  0.70 (0.29), residues: 294
  loop : -0.16 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 182 
 TYR   0.018   0.002   TYR S 103 
 PHE   0.026   0.002   PHE R 205 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.17 ( 8755)
  covalent geometry    : angle       0.59593 /  0.33 (11931)
  SS BOND              : bond        0.01087 /  0.52 (    2)
  SS BOND              : angle       2.24844 /  1.02 (    4)
  hydrogen bonds       : bond        0.05607 /  3.93 (  472)
  hydrogen bonds       : angle       4.67891 /  3.26 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B  217 MET cc_start: 0.8602 (pmm) cc_final: 0.8333 (ppp)
REVERT: B  226 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8522 (mp0)
REVERT: R  207 MET cc_start: 0.6812 (mmm) cc_final: 0.6441 (mmm)
REVERT: R  212 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5112 (mtm180)
REVERT: A  284 THR cc_start: 0.7721 (m) cc_final: 0.7477 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 142
  average time/residue: 0.5532
  time to fit residues: 83.4635
Evaluate side-chains
  151 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  212 ARG
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain R residue  374 ILE
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [97, 18, 63, 105, 45, 28, 26, 95, 79, 50, 37]
   chunk 97 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 105 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 126 ASN
R 158 ASN
R 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.179957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118104 restraints weight = 7624.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.72
r_work: 0.3152 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8757  Z= 0.134
  Angle     :  0.543   8.308  11935  Z= 0.301
  Chirality :  0.043   0.176   1392
  Planarity :  0.004   0.051   1511
  Dihedral  :  4.575  22.598   1237
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.11 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.81 (0.25), residues: 1132
  helix:  2.97 (0.24), residues: 396
  sheet:  0.70 (0.29), residues: 293
  loop : -0.08 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 182 
 TYR   0.016   0.001   TYR S 178 
 PHE   0.027   0.002   PHE R 205 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.13 ( 8755)
  covalent geometry    : angle       0.54203 /  0.30 (11931)
  SS BOND              : bond        0.00852 /  0.41 (    2)
  SS BOND              : angle       2.14065 /  0.99 (    4)
  hydrogen bonds       : bond        0.04981 /  3.49 (  472)
  hydrogen bonds       : angle       4.52307 /  3.15 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B  217 MET cc_start: 0.8614 (pmm) cc_final: 0.8410 (ppp)
REVERT: B  226 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8518 (mp0)
REVERT: R  207 MET cc_start: 0.6740 (mmm) cc_final: 0.6351 (mmm)
REVERT: R  212 ARG cc_start: 0.5683 (OUTLIER) cc_final: 0.5205 (mtm180)
  outliers start: 19
  outliers final: 16
  residues processed: 138
  average time/residue: 0.5736
  time to fit residues: 84.0296
Evaluate side-chains
  147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  212 ARG
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [66, 82, 21, 60, 29, 97, 101, 31, 111, 47, 78]
   chunk 66 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 126 ASN
R 158 ASN
R 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.179529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119150 restraints weight = 7655.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.69
r_work: 0.3135 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8757  Z= 0.147
  Angle     :  0.570   9.651  11935  Z= 0.314
  Chirality :  0.044   0.191   1392
  Planarity :  0.004   0.051   1511
  Dihedral  :  4.651  22.251   1237
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.47 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.77 (0.25), residues: 1132
  helix:  2.92 (0.24), residues: 396
  sheet:  0.70 (0.29), residues: 293
  loop : -0.08 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 182 
 TYR   0.017   0.002   TYR S 103 
 PHE   0.028   0.002   PHE R 205 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.15 ( 8755)
  covalent geometry    : angle       0.56856 /  0.31 (11931)
  SS BOND              : bond        0.00995 /  0.48 (    2)
  SS BOND              : angle       2.42285 /  1.12 (    4)
  hydrogen bonds       : bond        0.05235 /  3.66 (  472)
  hydrogen bonds       : angle       4.59545 /  3.20 ( 1341)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B  226 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8533 (mp0)
REVERT: R  207 MET cc_start: 0.6734 (mmm) cc_final: 0.6345 (mmm)
REVERT: R  212 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.5167 (mtm180)
REVERT: S    6 GLU cc_start: 0.8666 (mp0) cc_final: 0.8445 (mp0)
  outliers start: 19
  outliers final: 16
  residues processed: 137
  average time/residue: 0.5808
  time to fit residues: 84.3188
Evaluate side-chains
  147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  212 ARG
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  253 SER
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  347 MET
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  372 ARG
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks: [40, 55, 29, 63, 31, 88, 67, 5, 80, 60, 56]
   chunk 40 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 266 HIS
C  18 GLN
R 126 ASN
R 158 ASN
R 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.178729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.116732 restraints weight = 7579.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.62
r_work: 0.3124 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8757  Z= 0.177
  Angle     :  0.613  10.342  11935  Z= 0.337
  Chirality :  0.045   0.164   1392
  Planarity :  0.004   0.052   1511
  Dihedral  :  4.807  22.251   1237
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.23 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 are not related in a simple way.
  whole:  1.72 (0.25), residues: 1132
  helix:  2.94 (0.24), residues: 389
  sheet:  0.66 (0.29), residues: 295
  loop : -0.12 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 182 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.029   0.002   PHE R 205 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.18 ( 8755)
  covalent geometry    : angle       0.61107 /  0.34 (11931)
  SS BOND              : bond        0.01146 /  0.55 (    2)
  SS BOND              : angle       2.72560 /  1.25 (    4)
  hydrogen bonds       : bond        0.05682 /  3.98 (  472)
  hydrogen bonds       : angle       4.69978 /  3.28 ( 1341)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5462.14 seconds
wall clock time: 93 minutes 8.82 seconds (5588.82 seconds total)