Starting phenix.real_space_refine
on Wed Sep 17 12:26:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjd_60141/09_2025/8zjd_60141.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5617      2.51       5
     N    1521      2.21       5
     O    1627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8820
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2204
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 268}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "L"
      Number of atoms: 94
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 94
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2555
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "S"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1741
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 386
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1840
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
  Time building chain proxies: 2.33, per 1000 atoms: 0.26
  Number of scatterers: 8820
  At special positions: 0
  Unit cell: (97.09, 115.34, 129.21, 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      55     16.00
     O    1627      8.00
     N    1521      7.00
     C    5617      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 191 " distance=2.33

  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: 0.96
  Conformation dependent library (CDL) restraints added in 368.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 13 sheets defined
      40.7% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'R' and resid 43 through 69
      removed outlier: 3.823A  pdb=" N   LEU R  47 " --> pdb=" O   TRP R  43 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG R  69 " --> pdb=" O   TYR R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 94
    Processing helix  chain 'R' and resid 95 through 103
      removed outlier: 3.624A  pdb=" N   ALA R 100 " --> pdb=" O   VAL R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 146
    Processing helix  chain 'R' and resid 148 through 152
      removed outlier: 3.571A  pdb=" N   HIS R 152 " --> pdb=" O   ARG R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 174
    Processing helix  chain 'R' and resid 175 through 180
      removed outlier: 4.307A  pdb=" N   ALA R 179 " --> pdb=" O   ALA R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 213
    Processing helix  chain 'R' and resid 213 through 234
    Processing helix  chain 'R' and resid 244 through 289
      removed outlier: 5.285A  pdb=" N   ALA R 256 " --> pdb=" O   GLU R 252 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL R 257 " --> pdb=" O   ARG R 253 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 298 through 324
      removed outlier: 3.729A  pdb=" N   SER R 316 " --> pdb=" O   SER R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 327 through 337
    Processing helix  chain 'L' and resid 212 through 216
    Processing helix  chain 'B' and resid 10 through 31
      removed outlier: 4.435A  pdb=" N   GLN B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 3.781A  pdb=" N   ILE B 275 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 27 through 31
    Processing helix  chain 'S' and resid 52 through 55
    Processing helix  chain 'S' and resid 61 through 64
      removed outlier: 3.588A  pdb=" N   LYS S  64 " --> pdb=" O   ASP S  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 61 through 64'
    Processing helix  chain 'S' and resid 73 through 75
      No H-bonds generated for 'chain 'S' and resid 73 through 75'
    Processing helix  chain 'S' and resid 86 through 90
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.580A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 43
    Processing helix  chain 'G' and resid 44 through 47
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.603A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 4.427A  pdb=" N   ILE A 219 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   HIS A 220 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 289 through 293
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 337 through 358
    Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 184
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57
      removed outlier: 4.171A  pdb=" N   PHE B 340 " --> pdb=" O   SER B 336 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B 336 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   CYS B 322 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.763A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.787A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 4.388A  pdb=" N   THR B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.798A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   THR B 226 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU B 215 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   MET B 222 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.620A  pdb=" N   MET B 267 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283
      removed outlier: 3.781A  pdb=" N   CYS B 299 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY B 311 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 2 through 5
      removed outlier: 5.411A  pdb=" N   GLY S  15 " --> pdb=" O   SER S  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 9 through 11
      removed outlier: 6.951A  pdb=" N   MET S  33 " --> pdb=" O   TYR S  49 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   TYR S  49 " --> pdb=" O   MET S  33 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TRP S  35 " --> pdb=" O   VAL S  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.714A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 192 through 197
      removed outlier: 9.849A  pdb=" N   SER A 227 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   MET A 229 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU A 231 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      removed outlier: 8.898A  pdb=" N   ALA A 233 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE A 228 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   PHE A 274 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   PHE A 230 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASN A 276 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL A 232 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1308 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: 1.47

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1432
        1.31 -     1.44: 2527
        1.44 -     1.56: 4973
        1.56 -     1.69: 1
        1.69 -     1.82: 79
  Bond restraints: 9012
  Sorted by residual:
  bond pdb=" CA  VAL R 138 "
       pdb=" C   VAL R 138 "
    ideal  model  delta    sigma   weight residual
    1.525  1.465  0.060 1.27e-02 6.20e+03 2.25e+01
  bond pdb=" C   ASP R 139 "
       pdb=" O   ASP R 139 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.19e-02 7.06e+03 1.61e+01
  bond pdb=" CA  LYS A 356 "
       pdb=" C   LYS A 356 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.056 1.40e-02 5.10e+03 1.59e+01
  bond pdb=" C   ARG R 140 "
       pdb=" O   ARG R 140 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.25e-02 6.40e+03 1.48e+01
  bond pdb=" CA  ASP R 139 "
       pdb=" C   ASP R 139 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.049 1.29e-02 6.01e+03 1.46e+01
  ... (remaining 9007 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11956
        1.92 -     3.83: 246
        3.83 -     5.75: 32
        5.75 -     7.67: 5
        7.67 -     9.59: 5
  Bond angle restraints: 12244
  Sorted by residual:
  angle pdb=" N   ASP B  81 "
        pdb=" CA  ASP B  81 "
        pdb=" C   ASP B  81 "
      ideal   model   delta    sigma   weight residual
     113.16  103.83    9.33 1.24e+00 6.50e-01 5.67e+01
  angle pdb=" N   TYR A 358 "
        pdb=" CA  TYR A 358 "
        pdb=" C   TYR A 358 "
      ideal   model   delta    sigma   weight residual
     112.97  106.95    6.02 1.06e+00 8.90e-01 3.22e+01
  angle pdb=" N   VAL R 249 "
        pdb=" CA  VAL R 249 "
        pdb=" C   VAL R 249 "
      ideal   model   delta    sigma   weight residual
     110.74  105.63    5.11 9.10e-01 1.21e+00 3.15e+01
  angle pdb=" N   VAL R 138 "
        pdb=" CA  VAL R 138 "
        pdb=" C   VAL R 138 "
      ideal   model   delta    sigma   weight residual
     113.16  106.38    6.78 1.49e+00 4.50e-01 2.07e+01
  angle pdb=" N   ASP R 139 "
        pdb=" CA  ASP R 139 "
        pdb=" C   ASP R 139 "
      ideal   model   delta    sigma   weight residual
     111.40  105.88    5.52 1.22e+00 6.72e-01 2.05e+01
  ... (remaining 12239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4796
       17.79 -    35.57: 397
       35.57 -    53.36: 100
       53.36 -    71.15: 14
       71.15 -    88.94: 10
  Dihedral angle restraints: 5317
    sinusoidal: 1999
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CB  CYS R 115 "
           pdb=" SG  CYS R 115 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    4.06   88.94     1      1.00e+01 1.00e-02 9.42e+01
  dihedral pdb=" CA  GLN S  12 "
           pdb=" C   GLN S  12 "
           pdb=" N   PRO S  13 "
           pdb=" CA  PRO S  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LYS B  83 "
           pdb=" C   LYS B  83 "
           pdb=" N   LEU B  84 "
           pdb=" CA  LEU B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 5314 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1300
       0.091 -    0.182: 84
       0.182 -    0.272: 6
       0.272 -    0.363: 2
       0.363 -    0.454: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASN A 359 "
            pdb=" N   ASN A 359 "
            pdb=" C   ASN A 359 "
            pdb=" CB  ASN A 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.15e+00
  chirality pdb=" CA  VAL R 249 "
            pdb=" N   VAL R 249 "
            pdb=" C   VAL R 249 "
            pdb=" CB  VAL R 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  LEU R 245 "
            pdb=" N   LEU R 245 "
            pdb=" C   LEU R 245 "
            pdb=" CB  LEU R 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 136 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.67e+00
        pdb=" C   MET R 136 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET R 136 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER R 137 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 256 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   ALA R 256 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ALA R 256 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL R 257 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 338 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.49e+00
        pdb=" C   ASP B 338 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASP B 338 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER B 339 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 839
        2.74 -     3.28: 9025
        3.28 -     3.82: 14756
        3.82 -     4.36: 17644
        4.36 -     4.90: 31154
  Nonbonded interactions: 73418
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" OG  SER A 288 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ARG R 297 "
            pdb=" OH  TYR L 211 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B 150 "
            pdb=" OD2 ASP B 191 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   VAL R  96 "
            pdb=" OG1 THR R  99 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ASP B 210 "
            pdb=" OD1 ASP B 210 "
     model   vdw
     2.322 3.040
  ... (remaining 73413 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.060
  Find NCS groups from input model:        0.040
  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:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
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      :  0.005   0.295   9013  Z= 0.317
  Angle     :  0.701  20.935  12246  Z= 0.409
  Chirality :  0.046   0.454   1393
  Planarity :  0.004   0.050   1557
  Dihedral  : 14.501  85.750   3172
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.67 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1121
  helix:  1.57 (0.26), residues: 417
  sheet:  0.27 (0.32), residues: 278
  loop : -0.34 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 219 
 TYR   0.015   0.001   TYR R  65 
 PHE   0.016   0.001   PHE L 220 
 TRP   0.013   0.001   TRP B 104 
 HIS   0.002   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9012)
  covalent geometry    : angle       0.67435 (12244)
  SS BOND              : bond        0.29486 (    1)
  SS BOND              : angle      14.87771 (    2)
  hydrogen bonds       : bond        0.17303 (  469)
  hydrogen bonds       : angle       6.66791 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 156
  time to evaluate  : 0.317 
Fit side-chains
REVERT: R   62 LEU cc_start: 0.8167 (mp) cc_final: 0.7961 (mp)
REVERT: R   71 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6734 (tptp)
REVERT: R   78 ASN cc_start: 0.8894 (m110) cc_final: 0.8665 (m110)
REVERT: R  253 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6590 (ttp-170)
REVERT: R  315 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0)
REVERT: B  222 MET cc_start: 0.7156 (ptt) cc_final: 0.6885 (ptm)
REVERT: B  273 ASN cc_start: 0.8509 (m110) cc_final: 0.8171 (m110)
REVERT: S   45 GLU cc_start: 0.7652 (tt0) cc_final: 0.7443 (tt0)
REVERT: G   31 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8693 (tptt)
REVERT: G   46 GLU cc_start: 0.8252 (mp0) cc_final: 0.7867 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 160
  average time/residue: 0.1137
  time to fit residues: 24.2188
Evaluate side-chains
  130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 CYS
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R  83 ASN
B 273 ASN
S  38 GLN
S 112 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.156962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.112921 restraints weight = 12417.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.94
r_work: 0.3298 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9013  Z= 0.136
  Angle     :  0.580   7.096  12246  Z= 0.306
  Chirality :  0.042   0.142   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  5.251  56.239   1250
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.46 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1121
  helix:  1.90 (0.26), residues: 409
  sheet:  0.35 (0.32), residues: 275
  loop : -0.31 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 219 
 TYR   0.015   0.002   TYR R  65 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9012)
  covalent geometry    : angle       0.58036 (12244)
  SS BOND              : bond        0.00659 (    1)
  SS BOND              : angle       1.03215 (    2)
  hydrogen bonds       : bond        0.04374 (  469)
  hydrogen bonds       : angle       4.90427 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.336 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6699 (tptp)
REVERT: R   78 ASN cc_start: 0.8938 (m-40) cc_final: 0.8725 (m110)
REVERT: R  212 LEU cc_start: 0.8197 (mp) cc_final: 0.7989 (mp)
REVERT: R  253 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6407 (ttp-170)
REVERT: R  305 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7993 (tmtt)
REVERT: B  222 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7048 (ptm)
REVERT: B  273 ASN cc_start: 0.8629 (m-40) cc_final: 0.8299 (m110)
REVERT: S   66 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7567 (ttp80)
REVERT: S   81 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7502 (tp-100)
REVERT: S   82 MET cc_start: 0.8588 (ptp) cc_final: 0.8313 (ptp)
REVERT: G   31 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8584 (tptt)
REVERT: G   46 GLU cc_start: 0.8311 (mp0) cc_final: 0.7992 (mp0)
REVERT: A  250 MET cc_start: 0.8221 (ttm) cc_final: 0.8013 (tpp)
  outliers start: 18
  outliers final: 10
  residues processed: 156
  average time/residue: 0.1020
  time to fit residues: 22.0412
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  305 LYS
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  213 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
S  38 GLN
S 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.150303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107339 restraints weight = 12362.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.89
r_work: 0.3212 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9013  Z= 0.225
  Angle     :  0.612   6.087  12246  Z= 0.319
  Chirality :  0.044   0.171   1393
  Planarity :  0.004   0.050   1557
  Dihedral  :  5.339  54.026   1249
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.89 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.25), residues: 1121
  helix:  1.89 (0.25), residues: 406
  sheet:  0.18 (0.32), residues: 279
  loop : -0.55 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S  86 
 TYR   0.023   0.002   TYR A 237 
 PHE   0.013   0.002   PHE S  28 
 TRP   0.011   0.001   TRP B 174 
 HIS   0.005   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 9012)
  covalent geometry    : angle       0.61146 (12244)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       0.90626 (    2)
  hydrogen bonds       : bond        0.04382 (  469)
  hydrogen bonds       : angle       4.72329 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.367 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6699 (tptp)
REVERT: R  212 LEU cc_start: 0.8316 (mp) cc_final: 0.8005 (mp)
REVERT: R  253 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6402 (ttp-170)
REVERT: B  222 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (ptm)
REVERT: B  273 ASN cc_start: 0.8743 (m-40) cc_final: 0.8457 (m110)
REVERT: B  274 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7718 (pp)
REVERT: S   81 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7518 (tp-100)
REVERT: G   46 GLU cc_start: 0.8279 (mp0) cc_final: 0.8022 (mp0)
  outliers start: 28
  outliers final: 15
  residues processed: 156
  average time/residue: 0.0971
  time to fit residues: 21.0603
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  213 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 89 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 300 ASN
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.152556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109751 restraints weight = 12484.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.90
r_work: 0.3261 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9013  Z= 0.143
  Angle     :  0.558   6.631  12246  Z= 0.290
  Chirality :  0.042   0.145   1393
  Planarity :  0.004   0.049   1557
  Dihedral  :  5.137  50.033   1249
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.40 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.25), residues: 1121
  helix:  1.95 (0.25), residues: 409
  sheet:  0.08 (0.32), residues: 277
  loop : -0.48 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 139 
 TYR   0.014   0.001   TYR R  65 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.005   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9012)
  covalent geometry    : angle       0.55833 (12244)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.44785 (    2)
  hydrogen bonds       : bond        0.03827 (  469)
  hydrogen bonds       : angle       4.56959 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.350 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6685 (tptp)
REVERT: R  160 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7110 (tt)
REVERT: R  212 LEU cc_start: 0.8269 (mp) cc_final: 0.8016 (mp)
REVERT: R  253 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6319 (ttp-170)
REVERT: R  305 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (tmtt)
REVERT: B  222 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7047 (ptm)
REVERT: B  273 ASN cc_start: 0.8728 (m-40) cc_final: 0.8437 (m110)
REVERT: S   81 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7388 (tp-100)
REVERT: S   86 ARG cc_start: 0.7353 (mtp85) cc_final: 0.6682 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8281 (mp0) cc_final: 0.7997 (mp0)
REVERT: A  335 ASP cc_start: 0.7789 (m-30) cc_final: 0.7530 (m-30)
  outliers start: 26
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0966
  time to fit residues: 21.2550
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  305 LYS
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  314 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 96 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
B  80 GLN
S  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.153920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110905 restraints weight = 12450.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.93
r_work: 0.3278 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9013  Z= 0.124
  Angle     :  0.535   6.670  12246  Z= 0.278
  Chirality :  0.041   0.138   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.953  48.392   1249
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.37 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1121
  helix:  2.06 (0.25), residues: 409
  sheet:  0.12 (0.32), residues: 269
  loop : -0.55 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 139 
 TYR   0.020   0.001   TYR B  64 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9012)
  covalent geometry    : angle       0.53476 (12244)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.35458 (    2)
  hydrogen bonds       : bond        0.03579 (  469)
  hydrogen bonds       : angle       4.46975 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.352 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.7049 (mmmt) cc_final: 0.6718 (tptp)
REVERT: R   78 ASN cc_start: 0.8704 (m-40) cc_final: 0.8492 (m110)
REVERT: R  160 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7147 (tt)
REVERT: R  212 LEU cc_start: 0.8314 (mp) cc_final: 0.8017 (mp)
REVERT: R  253 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6330 (ttp-170)
REVERT: B  222 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7084 (ptm)
REVERT: B  273 ASN cc_start: 0.8723 (m-40) cc_final: 0.8428 (m110)
REVERT: B  274 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7693 (pp)
REVERT: S   81 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7371 (tp-100)
REVERT: S   86 ARG cc_start: 0.7426 (mtp85) cc_final: 0.6758 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8257 (mp0) cc_final: 0.7978 (mp0)
REVERT: A  335 ASP cc_start: 0.7817 (m-30) cc_final: 0.7540 (m-30)
  outliers start: 23
  outliers final: 17
  residues processed: 156
  average time/residue: 0.0990
  time to fit residues: 21.5406
Evaluate side-chains
  154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 ASN
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 75 optimal weight:    0.4980
   chunk 99 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 109 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.113320 restraints weight = 12495.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.97
r_work: 0.3293 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9013  Z= 0.106
  Angle     :  0.531   8.818  12246  Z= 0.273
  Chirality :  0.041   0.138   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.722  47.269   1247
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.80 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.25), residues: 1121
  helix:  2.15 (0.25), residues: 409
  sheet:  0.11 (0.32), residues: 269
  loop : -0.54 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 139 
 TYR   0.017   0.001   TYR R 190 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.014   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9012)
  covalent geometry    : angle       0.53141 (12244)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.28500 (    2)
  hydrogen bonds       : bond        0.03394 (  469)
  hydrogen bonds       : angle       4.40609 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7060 (mmmt) cc_final: 0.6680 (tptp)
REVERT: R   78 ASN cc_start: 0.8705 (m-40) cc_final: 0.8504 (m110)
REVERT: R  212 LEU cc_start: 0.8329 (mp) cc_final: 0.7983 (mp)
REVERT: R  253 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6316 (ttp-110)
REVERT: B  222 MET cc_start: 0.7373 (ptt) cc_final: 0.7106 (ptm)
REVERT: B  273 ASN cc_start: 0.8707 (m-40) cc_final: 0.8424 (m110)
REVERT: B  274 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (pp)
REVERT: B  280 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8158 (m)
REVERT: S   86 ARG cc_start: 0.7513 (mtp85) cc_final: 0.6860 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8278 (mp0) cc_final: 0.7991 (mp0)
  outliers start: 26
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0975
  time to fit residues: 21.9017
Evaluate side-chains
  157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
S  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.154329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.111152 restraints weight = 12546.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.96
r_work: 0.3255 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9013  Z= 0.152
  Angle     :  0.561   9.166  12246  Z= 0.288
  Chirality :  0.042   0.161   1393
  Planarity :  0.004   0.054   1557
  Dihedral  :  4.747  47.496   1247
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.09 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1121
  helix:  2.09 (0.25), residues: 410
  sheet:  0.02 (0.32), residues: 276
  loop : -0.53 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  29 
 TYR   0.017   0.001   TYR B  64 
 PHE   0.010   0.001   PHE B 246 
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9012)
  covalent geometry    : angle       0.56122 (12244)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.29849 (    2)
  hydrogen bonds       : bond        0.03628 (  469)
  hydrogen bonds       : angle       4.45034 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6957 (mmmt) cc_final: 0.6588 (tptp)
REVERT: R  212 LEU cc_start: 0.8337 (mp) cc_final: 0.8056 (mp)
REVERT: R  253 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6260 (ttp-110)
REVERT: B  222 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7128 (ptm)
REVERT: B  225 GLN cc_start: 0.8407 (mp10) cc_final: 0.8131 (mp10)
REVERT: B  273 ASN cc_start: 0.8742 (m-40) cc_final: 0.8443 (m110)
REVERT: B  274 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7693 (pp)
REVERT: B  280 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8222 (m)
REVERT: S   86 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6872 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8245 (mp0) cc_final: 0.7958 (mp0)
REVERT: A  250 MET cc_start: 0.8078 (ttm) cc_final: 0.7835 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 157
  average time/residue: 0.0961
  time to fit residues: 21.1228
Evaluate side-chains
  157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
S  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.155203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112306 restraints weight = 12468.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.95
r_work: 0.3275 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9013  Z= 0.126
  Angle     :  0.547   9.595  12246  Z= 0.279
  Chirality :  0.041   0.161   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.643  46.040   1247
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.42 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.25), residues: 1121
  helix:  2.14 (0.25), residues: 410
  sheet:  0.05 (0.32), residues: 268
  loop : -0.56 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 139 
 TYR   0.014   0.001   TYR B  64 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9012)
  covalent geometry    : angle       0.54718 (12244)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.31417 (    2)
  hydrogen bonds       : bond        0.03450 (  469)
  hydrogen bonds       : angle       4.41728 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6967 (mmmt) cc_final: 0.6608 (tptp)
REVERT: R  212 LEU cc_start: 0.8315 (mp) cc_final: 0.8043 (mp)
REVERT: R  253 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6244 (ttp-110)
REVERT: B  222 MET cc_start: 0.7414 (ptt) cc_final: 0.7156 (ptm)
REVERT: B  273 ASN cc_start: 0.8732 (m-40) cc_final: 0.8434 (m110)
REVERT: B  274 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7666 (pp)
REVERT: B  280 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8208 (m)
REVERT: S   37 ARG cc_start: 0.8964 (ptt180) cc_final: 0.8667 (ptt180)
REVERT: S   86 ARG cc_start: 0.7509 (mtp85) cc_final: 0.6902 (mtt-85)
REVERT: A  250 MET cc_start: 0.8098 (ttm) cc_final: 0.7819 (tpp)
  outliers start: 19
  outliers final: 15
  residues processed: 154
  average time/residue: 0.0979
  time to fit residues: 20.9932
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 109 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.153541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.111603 restraints weight = 12707.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.89
r_work: 0.3267 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9013  Z= 0.125
  Angle     :  0.549  10.103  12246  Z= 0.279
  Chirality :  0.041   0.161   1393
  Planarity :  0.004   0.054   1557
  Dihedral  :  4.588  45.887   1247
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.31 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.25), residues: 1121
  helix:  2.20 (0.25), residues: 409
  sheet:  0.10 (0.32), residues: 267
  loop : -0.52 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 302 
 TYR   0.013   0.001   TYR B  64 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.003   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9012)
  covalent geometry    : angle       0.54891 (12244)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.30285 (    2)
  hydrogen bonds       : bond        0.03399 (  469)
  hydrogen bonds       : angle       4.38343 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6580 (tptp)
REVERT: R  212 LEU cc_start: 0.8303 (mp) cc_final: 0.8029 (mp)
REVERT: R  253 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6210 (ttp-110)
REVERT: B  222 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7134 (ptm)
REVERT: B  225 GLN cc_start: 0.8385 (mp10) cc_final: 0.8136 (mp10)
REVERT: B  273 ASN cc_start: 0.8726 (m-40) cc_final: 0.8423 (m110)
REVERT: B  274 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7663 (pp)
REVERT: B  280 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8161 (m)
REVERT: S   37 ARG cc_start: 0.8926 (ptt180) cc_final: 0.8654 (ptt180)
REVERT: S   64 LYS cc_start: 0.8839 (tppp) cc_final: 0.7999 (tppt)
REVERT: S   66 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7213 (ttm110)
REVERT: S   86 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6883 (mtt-85)
REVERT: A  250 MET cc_start: 0.8101 (ttm) cc_final: 0.7827 (tpp)
  outliers start: 20
  outliers final: 15
  residues processed: 154
  average time/residue: 0.0956
  time to fit residues: 20.4009
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 73 optimal weight:    9.9990
   chunk 98 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 92 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.153413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.111499 restraints weight = 12647.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.89
r_work: 0.3264 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9013  Z= 0.132
  Angle     :  0.556  10.884  12246  Z= 0.284
  Chirality :  0.041   0.155   1393
  Planarity :  0.004   0.053   1557
  Dihedral  :  4.596  45.633   1247
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.42 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.25), residues: 1121
  helix:  2.18 (0.25), residues: 409
  sheet:  0.10 (0.32), residues: 269
  loop : -0.52 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  29 
 TYR   0.013   0.001   TYR B  64 
 PHE   0.010   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.003   0.001   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9012)
  covalent geometry    : angle       0.55627 (12244)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.31127 (    2)
  hydrogen bonds       : bond        0.03445 (  469)
  hydrogen bonds       : angle       4.38650 ( 1308)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6516 (tptp)
REVERT: R  212 LEU cc_start: 0.8298 (mp) cc_final: 0.8031 (mp)
REVERT: R  253 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6236 (ttp-110)
REVERT: B  222 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (ptm)
REVERT: B  225 GLN cc_start: 0.8393 (mp10) cc_final: 0.8140 (mp10)
REVERT: B  273 ASN cc_start: 0.8713 (m-40) cc_final: 0.8409 (m110)
REVERT: B  274 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7663 (pp)
REVERT: B  280 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8152 (m)
REVERT: S   37 ARG cc_start: 0.8922 (ptt180) cc_final: 0.8661 (ptt180)
REVERT: S   64 LYS cc_start: 0.8854 (tppp) cc_final: 0.8096 (tppt)
REVERT: S   66 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7210 (ttm110)
REVERT: S   86 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6873 (mtt-85)
REVERT: A  250 MET cc_start: 0.8128 (ttm) cc_final: 0.7853 (tpp)
  outliers start: 19
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0956
  time to fit residues: 20.4127
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 63 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.150690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.108443 restraints weight = 12439.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.92
r_work: 0.3237 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9013  Z= 0.168
  Angle     :  0.580  11.073  12246  Z= 0.297
  Chirality :  0.042   0.183   1393
  Planarity :  0.004   0.054   1557
  Dihedral  :  4.720  45.303   1247
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.63 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1121
  helix:  2.16 (0.25), residues: 406
  sheet:  0.08 (0.32), residues: 275
  loop : -0.56 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  29 
 TYR   0.020   0.002   TYR B  64 
 PHE   0.010   0.001   PHE S  28 
 TRP   0.011   0.001   TRP B 174 
 HIS   0.003   0.001   HIS S  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9012)
  covalent geometry    : angle       0.58011 (12244)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.37849 (    2)
  hydrogen bonds       : bond        0.03650 (  469)
  hydrogen bonds       : angle       4.45521 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2506.26 seconds
wall clock time: 43 minutes 47.05 seconds (2627.05 seconds total)