Starting phenix.real_space_refine
on Sat Aug 23 05:16:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g4f_51037/08_2025/9g4f_51037.map"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      38      5.16       5
     C    6330      2.51       5
     N    1579      2.21       5
     O    1713      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9660
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3183
          Classifications: {'peptide': 391}
          Link IDs: {'PTRANS': 14, 'TRANS': 376}
    Chain: "B"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3183
          Classifications: {'peptide': 391}
          Link IDs: {'PTRANS': 14, 'TRANS': 376}
    Chain: "C"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1658
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 206}
    Chain: "D"
      Number of atoms: 1636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1636
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
  Time building chain proxies: 1.89, per 1000 atoms: 0.20
  Number of scatterers: 9660
  At special positions: 0
  Unit cell: (70.52, 99.76, 178.02, 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      38     16.00
     O    1713      8.00
     N    1579      7.00
     C    6330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  16 " - pdb=" SG  CYS C  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 130 " - pdb=" SG  CYS D 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 197 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  87 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 193 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 293.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 13 sheets defined
      57.4% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
      removed outlier: 3.955A  pdb=" N   LEU A  14 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 48 through 53
      removed outlier: 3.554A  pdb=" N   ARG A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE A  52 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TRP A  53 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 53'
    Processing helix  chain 'A' and resid 54 through 79
      removed outlier: 4.516A  pdb=" N   PHE A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 125
      removed outlier: 4.182A  pdb=" N   THR A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ALA A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
    Processing helix  chain 'A' and resid 126 through 129
      removed outlier: 3.895A  pdb=" N   VAL A 129 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 126 through 129'
    Processing helix  chain 'A' and resid 130 through 177
      removed outlier: 4.236A  pdb=" N   PHE A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ILE A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ASN A 177 " --> pdb=" O   TYR A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 186 through 227
      removed outlier: 5.764A  pdb=" N   THR A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   MET A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 241 through 262
      removed outlier: 3.661A  pdb=" N   VAL A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 289
      removed outlier: 3.791A  pdb=" N   LEU A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLY A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASP A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 308
      removed outlier: 3.551A  pdb=" N   ASN A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 316 through 337
      removed outlier: 3.790A  pdb=" N   ALA A 322 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG A 323 " --> pdb=" O   PHE A 319 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ASN A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL A 332 " --> pdb=" O   GLN A 328 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 334 " --> pdb=" O   ASP A 330 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LEU A 337 " --> pdb=" O   PHE A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 351 through 366
      removed outlier: 3.516A  pdb=" N   ILE A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 371
      removed outlier: 3.644A  pdb=" N   ILE A 370 " --> pdb=" O   GLN A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 377
      removed outlier: 3.736A  pdb=" N   THR A 375 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 389
    Processing helix  chain 'B' and resid 10 through 29
      removed outlier: 4.318A  pdb=" N   LEU B  14 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B  29 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 50 through 53
      removed outlier: 3.939A  pdb=" N   TRP B  53 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 50 through 53'
    Processing helix  chain 'B' and resid 54 through 79
      removed outlier: 3.896A  pdb=" N   PHE B  60 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TRP B  75 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER B  79 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 125
      removed outlier: 4.572A  pdb=" N   THR B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ALA B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
      Proline residue:  B 114  - end of helix
    Processing helix  chain 'B' and resid 130 through 177
      removed outlier: 4.122A  pdb=" N   PHE B 134 " --> pdb=" O   THR B 130 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE B 147 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASN B 177 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 183
      removed outlier: 3.575A  pdb=" N   LEU B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   HIS B 183 " --> pdb=" O   GLN B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 227
      removed outlier: 3.588A  pdb=" N   ARG B 190 " --> pdb=" O   GLY B 186 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   THR B 195 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   MET B 196 " --> pdb=" O   GLN B 192 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 241 through 259
    Processing helix  chain 'B' and resid 264 through 289
      removed outlier: 3.611A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR B 285 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY B 286 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU B 287 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASP B 289 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 315
      removed outlier: 3.729A  pdb=" N   ASN B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   TYR B 309 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ARG B 311 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   LEU B 312 " --> pdb=" O   ASN B 308 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR B 313 " --> pdb=" O   TYR B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 337
      removed outlier: 3.939A  pdb=" N   ALA B 322 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ARG B 323 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ASN B 331 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL B 332 " --> pdb=" O   GLN B 328 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY B 334 " --> pdb=" O   ASP B 330 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   LEU B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU B 337 " --> pdb=" O   PHE B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
    Processing helix  chain 'B' and resid 351 through 366
      removed outlier: 3.796A  pdb=" N   ILE B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 373 through 376
    Processing helix  chain 'B' and resid 377 through 389
      removed outlier: 3.914A  pdb=" N   SER B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 26
      removed outlier: 3.818A  pdb=" N   THR C  26 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 158 through 160
      No H-bonds generated for 'chain 'C' and resid 158 through 160'
    Processing helix  chain 'D' and resid 120 through 126
      removed outlier: 3.556A  pdb=" N   THR D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 187
      removed outlier: 3.537A  pdb=" N   ARG D 187 " --> pdb=" O   ASP D 183 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233
      removed outlier: 3.862A  pdb=" N   GLY A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233
    Processing sheet with id=AA3, first strand: chain 'C' and resid -3 through 0
      removed outlier: 3.832A  pdb=" N   THR C  17 " --> pdb=" O   LEU C  -1 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 54
      removed outlier: 6.827A  pdb=" N   TRP C  30 " --> pdb=" O   ILE C  42 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 122 through 126
      removed outlier: 3.763A  pdb=" N   GLY C 141 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   CYS C 142 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126
      removed outlier: 3.763A  pdb=" N   GLY C 141 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL C 171 " --> pdb=" O   THR C 178 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 153 through 156
      removed outlier: 3.723A  pdb=" N   LYS C 210 " --> pdb=" O   CYS C 197 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 7
      removed outlier: 3.735A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   TYR D  70 " --> pdb=" O   CYS D  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 52 through 53
      removed outlier: 3.842A  pdb=" N   ILE D  47 " --> pdb=" O   TRP D  34 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TRP D  34 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 85
      removed outlier: 4.202A  pdb=" N   TYR D  85 " --> pdb=" O   THR D 101 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR D 101 " --> pdb=" O   TYR D  85 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'D' and resid 113 through 117
      removed outlier: 3.558A  pdb=" N   VAL D 132 " --> pdb=" O   PHE D 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER D 161 " --> pdb=" O   SER D 175 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU D 159 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153
      removed outlier: 4.048A  pdb=" N   ASN D 144 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   TYR D 191 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE D 208 " --> pdb=" O   TYR D 191 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   HIS D 197 " --> pdb=" O   SER D 202 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   SER D 202 " --> pdb=" O   HIS D 197 " (cutoff:3.500A)

    552 hydrogen bonds defined for protein.
    1596 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: 1.30

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2783
        1.33 -     1.46: 2885
        1.46 -     1.59: 4214
        1.59 -     1.72: 0
        1.72 -     1.85: 64
  Bond restraints: 9946
  Sorted by residual:
  bond pdb=" CB  TRP D  90 "
       pdb=" CG  TRP D  90 "
    ideal  model  delta    sigma   weight residual
    1.498  1.362  0.136 3.10e-02 1.04e+03 1.93e+01
  bond pdb=" CB  TRP D  46 "
       pdb=" CG  TRP D  46 "
    ideal  model  delta    sigma   weight residual
    1.498  1.406  0.092 3.10e-02 1.04e+03 8.88e+00
  bond pdb=" CA  SER A 227 "
       pdb=" C   SER A 227 "
    ideal  model  delta    sigma   weight residual
    1.523  1.478  0.045 1.80e-02 3.09e+03 6.21e+00
  bond pdb=" CG1 ILE A  88 "
       pdb=" CD1 ILE A  88 "
    ideal  model  delta    sigma   weight residual
    1.513  1.420  0.093 3.90e-02 6.57e+02 5.69e+00
  bond pdb=" CA  SER B 227 "
       pdb=" C   SER B 227 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.041 1.80e-02 3.09e+03 5.12e+00
  ... (remaining 9941 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 12759
        1.82 -     3.65: 689
        3.65 -     5.47: 88
        5.47 -     7.30: 25
        7.30 -     9.12: 4
  Bond angle restraints: 13565
  Sorted by residual:
  angle pdb=" C   GLN A 192 "
        pdb=" N   GLU A 193 "
        pdb=" CA  GLU A 193 "
      ideal   model   delta    sigma   weight residual
     122.08  113.47    8.61 1.53e+00 4.27e-01 3.17e+01
  angle pdb=" N   HIS B 315 "
        pdb=" CA  HIS B 315 "
        pdb=" C   HIS B 315 "
      ideal   model   delta    sigma   weight residual
     113.20  107.20    6.00 1.36e+00 5.41e-01 1.94e+01
  angle pdb=" N   SER D  30 "
        pdb=" CA  SER D  30 "
        pdb=" CB  SER D  30 "
      ideal   model   delta    sigma   weight residual
     114.17  109.95    4.22 1.14e+00 7.69e-01 1.37e+01
  angle pdb=" N   PHE B   5 "
        pdb=" CA  PHE B   5 "
        pdb=" CB  PHE B   5 "
      ideal   model   delta    sigma   weight residual
     111.20  105.37    5.83 1.62e+00 3.81e-01 1.29e+01
  angle pdb=" CA  TYR A 309 "
        pdb=" CB  TYR A 309 "
        pdb=" CG  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     113.90  119.90   -6.00 1.80e+00 3.09e-01 1.11e+01
  ... (remaining 13560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 5180
       17.95 -    35.89: 446
       35.89 -    53.84: 84
       53.84 -    71.78: 12
       71.78 -    89.73: 5
  Dihedral angle restraints: 5727
    sinusoidal: 2184
      harmonic: 3543
  Sorted by residual:
  dihedral pdb=" CA  ASN D  93 "
           pdb=" C   ASN D  93 "
           pdb=" N   PRO D  94 "
           pdb=" CA  PRO D  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  112.38   67.62     0      5.00e+00 4.00e-02 1.83e+02
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 193 "
           pdb=" CB  CYS D 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.69   46.31     1      1.00e+01 1.00e-02 2.97e+01
  dihedral pdb=" CA  ALA B 290 "
           pdb=" C   ALA B 290 "
           pdb=" N   THR B 291 "
           pdb=" CA  THR B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.57  -25.43     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 5724 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 964
       0.046 -    0.092: 419
       0.092 -    0.138: 102
       0.138 -    0.184: 26
       0.184 -    0.230: 4
  Chirality restraints: 1515
  Sorted by residual:
  chirality pdb=" CB  VAL B 332 "
            pdb=" CA  VAL B 332 "
            pdb=" CG1 VAL B 332 "
            pdb=" CG2 VAL B 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  TYR A 112 "
            pdb=" N   TYR A 112 "
            pdb=" C   TYR A 112 "
            pdb=" CB  TYR A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 1512 not shown)

  Planarity restraints: 1682
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B   5 "    0.034 2.00e-02 2.50e+03   2.69e-02 1.27e+01
        pdb=" CG  PHE B   5 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD1 PHE B   5 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B   5 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B   5 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B   5 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B   5 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  53 "   -0.017 2.00e-02 2.50e+03   2.18e-02 1.19e+01
        pdb=" CG  TRP B  53 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  53 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  53 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  53 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  53 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  90 "    0.022 2.00e-02 2.50e+03   1.84e-02 8.49e+00
        pdb=" CG  TRP D  90 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  90 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  90 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  90 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  90 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  90 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1679 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 232
        2.68 -     3.24: 9528
        3.24 -     3.79: 14000
        3.79 -     4.35: 16866
        4.35 -     4.90: 29558
  Nonbonded interactions: 70184
  Sorted by model distance:
  nonbonded pdb=" O   SER B   4 "
            pdb=" NE2 HIS B  81 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" O   SER A   4 "
            pdb=" NE2 HIS A  81 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" NH2 ARG C  34 "
            pdb=" OE2 GLU C  40 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" NE2 GLN A 189 "
            pdb=" OE2 GLU A 193 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG1 THR A 294 "
            pdb=" OG1 THR A 297 "
     model   vdw
     2.222 3.040
  ... (remaining 70179 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.480
  Find NCS groups from input model:        0.100
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
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      :  0.012   0.136   9951  Z= 0.484
  Angle     :  0.948   9.122  13575  Z= 0.538
  Chirality :  0.054   0.230   1515
  Planarity :  0.006   0.070   1682
  Dihedral  : 13.942  89.726   3442
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.24), residues: 1207
  helix:  0.23 (0.20), residues: 635
  sheet: -0.36 (0.39), residues: 187
  loop : -2.31 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 190 
 TYR   0.040   0.003   TYR A 112 
 PHE   0.061   0.003   PHE B   5 
 TRP   0.057   0.004   TRP B  53 
 HIS   0.009   0.002   HIS D 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.01184 ( 9946)
  covalent geometry    : angle       0.94499 (13565)
  SS BOND              : bond        0.01232 (    5)
  SS BOND              : angle       2.83677 (   10)
  hydrogen bonds       : bond        0.20091 (  547)
  hydrogen bonds       : angle       6.77259 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 TRP cc_start: 0.7855 (p-90) cc_final: 0.7415 (p-90)
REVERT: B  196 MET cc_start: 0.8572 (tpt) cc_final: 0.8345 (tpp)
REVERT: B  289 ASP cc_start: 0.8819 (p0) cc_final: 0.8507 (p0)
REVERT: C  173 GLN cc_start: 0.8334 (tt0) cc_final: 0.7982 (pp30)
REVERT: D  184 GLU cc_start: 0.8776 (tt0) cc_final: 0.8227 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1107
  time to fit residues: 18.6594
Evaluate side-chains
  87 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 109 ASN
B 354 GLN
C 166 HIS
C 198 ASN
** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.093465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.073169 restraints weight = 26443.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.074484 restraints weight = 13145.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.075552 restraints weight = 9134.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.075711 restraints weight = 7574.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.076240 restraints weight = 7047.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9951  Z= 0.160
  Angle     :  0.620   7.142  13575  Z= 0.337
  Chirality :  0.043   0.177   1515
  Planarity :  0.005   0.069   1682
  Dihedral  :  5.167  57.012   1327
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.12 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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: -0.03 (0.24), residues: 1207
  helix:  1.04 (0.21), residues: 634
  sheet:  0.08 (0.39), residues: 190
  loop : -1.88 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  99 
 TYR   0.011   0.001   TYR A 112 
 PHE   0.012   0.001   PHE B   5 
 TRP   0.027   0.002   TRP D  90 
 HIS   0.006   0.001   HIS D 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9946)
  covalent geometry    : angle       0.61895 (13565)
  SS BOND              : bond        0.00944 (    5)
  SS BOND              : angle       1.31727 (   10)
  hydrogen bonds       : bond        0.07980 (  547)
  hydrogen bonds       : angle       4.94150 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8807 (Cg_endo) cc_final: 0.8482 (Cg_exo)
REVERT: A  289 ASP cc_start: 0.7928 (t0) cc_final: 0.7699 (t70)
REVERT: A  373 TRP cc_start: 0.7850 (p-90) cc_final: 0.7086 (p-90)
REVERT: A  378 GLU cc_start: 0.8352 (mp0) cc_final: 0.7850 (mp0)
REVERT: B  196 MET cc_start: 0.7983 (tpt) cc_final: 0.7643 (tpp)
REVERT: B  380 MET cc_start: 0.7885 (mpp) cc_final: 0.7680 (mpp)
REVERT: C  173 GLN cc_start: 0.8498 (tt0) cc_final: 0.8049 (pp30)
REVERT: D  174 MET cc_start: 0.8293 (ttt) cc_final: 0.7622 (tpt)
REVERT: D  184 GLU cc_start: 0.9206 (tt0) cc_final: 0.8986 (tp30)
REVERT: D  187 ARG cc_start: 0.8986 (mtm180) cc_final: 0.8356 (mtm180)
REVERT: D  194 GLU cc_start: 0.8451 (tp30) cc_final: 0.7947 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 116
  average time/residue: 0.0963
  time to fit residues: 15.8671
Evaluate side-chains
  97 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 120 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
A 308 ASN
B 161 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.091785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071429 restraints weight = 26724.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.072991 restraints weight = 13619.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073839 restraints weight = 9417.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.074002 restraints weight = 8031.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.074298 restraints weight = 7586.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9951  Z= 0.173
  Angle     :  0.584   6.870  13575  Z= 0.314
  Chirality :  0.042   0.161   1515
  Planarity :  0.005   0.070   1682
  Dihedral  :  4.885  55.912   1327
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.54 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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:  0.35 (0.25), residues: 1207
  helix:  1.31 (0.21), residues: 634
  sheet:  0.36 (0.38), residues: 194
  loop : -1.69 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  76 
 TYR   0.012   0.001   TYR C  27 
 PHE   0.016   0.001   PHE A   5 
 TRP   0.033   0.001   TRP D  90 
 HIS   0.003   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9946)
  covalent geometry    : angle       0.58366 (13565)
  SS BOND              : bond        0.01099 (    5)
  SS BOND              : angle       1.15838 (   10)
  hydrogen bonds       : bond        0.07511 (  547)
  hydrogen bonds       : angle       4.69753 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8980 (Cg_endo) cc_final: 0.8720 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7966 (t80)
REVERT: A  373 TRP cc_start: 0.7788 (p-90) cc_final: 0.7166 (p-90)
REVERT: A  378 GLU cc_start: 0.8188 (mp0) cc_final: 0.7810 (mp0)
REVERT: B  196 MET cc_start: 0.8001 (tpt) cc_final: 0.7653 (tpp)
REVERT: B  203 GLU cc_start: 0.8633 (tp30) cc_final: 0.8373 (tm-30)
REVERT: C  173 GLN cc_start: 0.8522 (tt0) cc_final: 0.8073 (pp30)
REVERT: D  174 MET cc_start: 0.8257 (ttt) cc_final: 0.7593 (tpt)
REVERT: D  194 GLU cc_start: 0.8460 (tp30) cc_final: 0.7972 (tp30)
  outliers start: 21
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0894
  time to fit residues: 14.1278
Evaluate side-chains
  105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain D residue   21 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 272 ASN
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.091376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.070793 restraints weight = 27076.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.072538 restraints weight = 13296.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073755 restraints weight = 8938.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.073877 restraints weight = 7468.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.074008 restraints weight = 6856.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9951  Z= 0.169
  Angle     :  0.569   7.391  13575  Z= 0.304
  Chirality :  0.041   0.155   1515
  Planarity :  0.005   0.066   1682
  Dihedral  :  4.768  57.121   1327
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.99 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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:  0.66 (0.25), residues: 1207
  helix:  1.53 (0.21), residues: 632
  sheet:  0.64 (0.39), residues: 194
  loop : -1.57 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  76 
 TYR   0.011   0.001   TYR C  27 
 PHE   0.016   0.001   PHE B 389 
 TRP   0.024   0.001   TRP D  90 
 HIS   0.003   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9946)
  covalent geometry    : angle       0.56854 (13565)
  SS BOND              : bond        0.00763 (    5)
  SS BOND              : angle       1.08043 (   10)
  hydrogen bonds       : bond        0.07223 (  547)
  hydrogen bonds       : angle       4.56553 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8978 (Cg_endo) cc_final: 0.8727 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8074 (t80)
REVERT: A  373 TRP cc_start: 0.7792 (p-90) cc_final: 0.7266 (p-90)
REVERT: A  378 GLU cc_start: 0.8195 (mp0) cc_final: 0.7819 (mp0)
REVERT: B  112 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7512 (t80)
REVERT: B  196 MET cc_start: 0.8027 (tpt) cc_final: 0.7629 (tpp)
REVERT: B  203 GLU cc_start: 0.8650 (tp30) cc_final: 0.8395 (tm-30)
REVERT: C  173 GLN cc_start: 0.8505 (tt0) cc_final: 0.8070 (pp30)
REVERT: D  174 MET cc_start: 0.8289 (ttt) cc_final: 0.7621 (tpt)
REVERT: D  194 GLU cc_start: 0.8504 (tp30) cc_final: 0.8047 (tp30)
  outliers start: 25
  outliers final: 18
  residues processed: 110
  average time/residue: 0.0861
  time to fit residues: 13.6702
Evaluate side-chains
  111 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
C 198 ASN
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.091242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.070912 restraints weight = 27094.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.072443 restraints weight = 13701.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.073280 restraints weight = 9466.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.073440 restraints weight = 8170.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073682 restraints weight = 7702.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9951  Z= 0.168
  Angle     :  0.572   8.339  13575  Z= 0.302
  Chirality :  0.041   0.162   1515
  Planarity :  0.005   0.069   1682
  Dihedral  :  4.660  56.411   1327
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.35 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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: 1207
  helix:  1.66 (0.20), residues: 632
  sheet:  0.60 (0.38), residues: 212
  loop : -1.49 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  76 
 TYR   0.011   0.001   TYR B  63 
 PHE   0.026   0.001   PHE B 389 
 TRP   0.016   0.001   TRP D  90 
 HIS   0.003   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9946)
  covalent geometry    : angle       0.57092 (13565)
  SS BOND              : bond        0.00792 (    5)
  SS BOND              : angle       1.19766 (   10)
  hydrogen bonds       : bond        0.07084 (  547)
  hydrogen bonds       : angle       4.47398 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8954 (Cg_endo) cc_final: 0.8715 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8201 (t80)
REVERT: A  373 TRP cc_start: 0.7808 (p-90) cc_final: 0.7203 (p-90)
REVERT: A  378 GLU cc_start: 0.8156 (mp0) cc_final: 0.7691 (mp0)
REVERT: B  112 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7485 (t80)
REVERT: B  196 MET cc_start: 0.8081 (tpt) cc_final: 0.7691 (tpp)
REVERT: B  203 GLU cc_start: 0.8666 (tp30) cc_final: 0.8424 (tm-30)
REVERT: B  226 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9096 (tt)
REVERT: C  173 GLN cc_start: 0.8515 (tt0) cc_final: 0.8127 (pp30)
REVERT: D  174 MET cc_start: 0.8331 (ttt) cc_final: 0.7730 (tpt)
REVERT: D  194 GLU cc_start: 0.8406 (tp30) cc_final: 0.7978 (tp30)
  outliers start: 29
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0908
  time to fit residues: 14.5909
Evaluate side-chains
  115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.087496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066222 restraints weight = 28201.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068338 restraints weight = 14151.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.069148 restraints weight = 9101.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.069227 restraints weight = 8343.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.069389 restraints weight = 7747.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9951  Z= 0.136
  Angle     :  0.550   8.782  13575  Z= 0.288
  Chirality :  0.040   0.162   1515
  Planarity :  0.004   0.067   1682
  Dihedral  :  4.490  55.362   1327
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.70 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.25), residues: 1207
  helix:  1.77 (0.20), residues: 640
  sheet:  0.65 (0.37), residues: 221
  loop : -1.37 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  76 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.025   0.001   PHE B 389 
 TRP   0.011   0.001   TRP B  53 
 HIS   0.022   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9946)
  covalent geometry    : angle       0.54922 (13565)
  SS BOND              : bond        0.00631 (    5)
  SS BOND              : angle       0.85847 (   10)
  hydrogen bonds       : bond        0.06507 (  547)
  hydrogen bonds       : angle       4.26768 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8905 (Cg_endo) cc_final: 0.8658 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8303 (t80)
REVERT: A  373 TRP cc_start: 0.7825 (p-90) cc_final: 0.7289 (p-90)
REVERT: B  112 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7513 (t80)
REVERT: B  196 MET cc_start: 0.7894 (tpt) cc_final: 0.7525 (tpp)
REVERT: B  203 GLU cc_start: 0.8616 (tp30) cc_final: 0.8369 (tm-30)
REVERT: B  226 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9022 (tt)
REVERT: C  102 MET cc_start: 0.8183 (mmm) cc_final: 0.7877 (mtt)
REVERT: C  173 GLN cc_start: 0.8572 (tt0) cc_final: 0.8192 (pp30)
REVERT: D   48 TYR cc_start: 0.8741 (t80) cc_final: 0.8356 (t80)
REVERT: D  174 MET cc_start: 0.8287 (ttt) cc_final: 0.7646 (tpt)
REVERT: D  194 GLU cc_start: 0.8489 (tp30) cc_final: 0.8085 (tp30)
  outliers start: 20
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0965
  time to fit residues: 15.0095
Evaluate side-chains
  107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 118 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
B 183 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.086887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.065767 restraints weight = 28385.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.067663 restraints weight = 14416.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.068386 restraints weight = 9693.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068523 restraints weight = 8825.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.068656 restraints weight = 8165.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9951  Z= 0.150
  Angle     :  0.567   9.539  13575  Z= 0.295
  Chirality :  0.040   0.159   1515
  Planarity :  0.004   0.070   1682
  Dihedral  :  4.446  55.267   1327
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.99 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.25), residues: 1207
  helix:  1.88 (0.20), residues: 638
  sheet:  0.68 (0.38), residues: 215
  loop : -1.45 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  76 
 TYR   0.010   0.001   TYR B  63 
 PHE   0.026   0.001   PHE B 389 
 TRP   0.011   0.001   TRP D  90 
 HIS   0.004   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9946)
  covalent geometry    : angle       0.56593 (13565)
  SS BOND              : bond        0.00662 (    5)
  SS BOND              : angle       1.11814 (   10)
  hydrogen bonds       : bond        0.06509 (  547)
  hydrogen bonds       : angle       4.26970 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8977 (Cg_endo) cc_final: 0.8723 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8329 (t80)
REVERT: A  373 TRP cc_start: 0.7815 (p-90) cc_final: 0.7277 (p-90)
REVERT: B  112 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7545 (t80)
REVERT: B  196 MET cc_start: 0.7959 (tpt) cc_final: 0.7619 (tpp)
REVERT: B  203 GLU cc_start: 0.8626 (tp30) cc_final: 0.8358 (tm-30)
REVERT: B  226 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8995 (tt)
REVERT: C  173 GLN cc_start: 0.8578 (tt0) cc_final: 0.8208 (pp30)
REVERT: D  174 MET cc_start: 0.8321 (ttt) cc_final: 0.7692 (tpt)
REVERT: D  183 ASP cc_start: 0.9299 (p0) cc_final: 0.9054 (p0)
REVERT: D  187 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8741 (ptp90)
REVERT: D  194 GLU cc_start: 0.8420 (tp30) cc_final: 0.8208 (tp30)
REVERT: D  205 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8789 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 106
  average time/residue: 0.0990
  time to fit residues: 15.0024
Evaluate side-chains
  109 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain D residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 101 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 97 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 84 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.087307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.066375 restraints weight = 28491.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.067801 restraints weight = 14690.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.068820 restraints weight = 10106.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.069120 restraints weight = 8744.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.069117 restraints weight = 7840.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9951  Z= 0.146
  Angle     :  0.560   8.926  13575  Z= 0.291
  Chirality :  0.040   0.161   1515
  Planarity :  0.004   0.068   1682
  Dihedral  :  4.417  55.328   1327
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.99 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.25), residues: 1207
  helix:  1.92 (0.20), residues: 638
  sheet:  0.64 (0.38), residues: 217
  loop : -1.40 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  76 
 TYR   0.010   0.001   TYR D  31 
 PHE   0.026   0.001   PHE B 389 
 TRP   0.010   0.001   TRP A  34 
 HIS   0.011   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9946)
  covalent geometry    : angle       0.55905 (13565)
  SS BOND              : bond        0.00670 (    5)
  SS BOND              : angle       1.09946 (   10)
  hydrogen bonds       : bond        0.06414 (  547)
  hydrogen bonds       : angle       4.22346 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8691 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8296 (t80)
REVERT: A  253 MET cc_start: 0.8352 (tpp) cc_final: 0.7540 (tmm)
REVERT: A  373 TRP cc_start: 0.7842 (p-90) cc_final: 0.7340 (p-90)
REVERT: B  112 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7570 (t80)
REVERT: B  196 MET cc_start: 0.7911 (tpt) cc_final: 0.7583 (tpp)
REVERT: B  203 GLU cc_start: 0.8620 (tp30) cc_final: 0.8355 (tm-30)
REVERT: B  226 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8986 (tt)
REVERT: C  173 GLN cc_start: 0.8526 (tt0) cc_final: 0.8196 (pp30)
REVERT: D   48 TYR cc_start: 0.8841 (t80) cc_final: 0.8416 (t80)
REVERT: D  166 ASP cc_start: 0.8550 (t70) cc_final: 0.8333 (t70)
REVERT: D  174 MET cc_start: 0.8326 (ttt) cc_final: 0.7641 (tpt)
REVERT: D  183 ASP cc_start: 0.9310 (p0) cc_final: 0.9089 (p0)
REVERT: D  187 ARG cc_start: 0.8977 (mtm180) cc_final: 0.8706 (ptp90)
REVERT: D  205 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8765 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1019
  time to fit residues: 15.7076
Evaluate side-chains
  108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain D residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0070
   chunk 12 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.086678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.065498 restraints weight = 28277.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.067417 restraints weight = 14518.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.068218 restraints weight = 9666.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.068324 restraints weight = 8808.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.068459 restraints weight = 8138.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9951  Z= 0.158
  Angle     :  0.577  11.402  13575  Z= 0.299
  Chirality :  0.040   0.165   1515
  Planarity :  0.004   0.070   1682
  Dihedral  :  4.440  55.645   1327
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.86 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.25), residues: 1207
  helix:  1.89 (0.20), residues: 644
  sheet:  0.61 (0.38), residues: 218
  loop : -1.49 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  76 
 TYR   0.012   0.001   TYR D  31 
 PHE   0.025   0.001   PHE B 389 
 TRP   0.011   0.001   TRP A  34 
 HIS   0.003   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9946)
  covalent geometry    : angle       0.57634 (13565)
  SS BOND              : bond        0.00776 (    5)
  SS BOND              : angle       1.13444 (   10)
  hydrogen bonds       : bond        0.06581 (  547)
  hydrogen bonds       : angle       4.27923 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8964 (Cg_endo) cc_final: 0.8741 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8303 (t80)
REVERT: A  253 MET cc_start: 0.8361 (tpp) cc_final: 0.7550 (tmm)
REVERT: A  373 TRP cc_start: 0.7858 (p-90) cc_final: 0.7397 (p-90)
REVERT: B  112 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: B  196 MET cc_start: 0.7954 (tpt) cc_final: 0.7590 (tpp)
REVERT: B  203 GLU cc_start: 0.8608 (tp30) cc_final: 0.8384 (tm-30)
REVERT: B  226 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8985 (tt)
REVERT: C  173 GLN cc_start: 0.8556 (tt0) cc_final: 0.8211 (pp30)
REVERT: D  166 ASP cc_start: 0.8676 (t70) cc_final: 0.8469 (t70)
REVERT: D  174 MET cc_start: 0.8355 (ttt) cc_final: 0.7702 (tpt)
REVERT: D  183 ASP cc_start: 0.9294 (p0) cc_final: 0.9076 (p0)
REVERT: D  187 ARG cc_start: 0.8956 (mtm180) cc_final: 0.8685 (ptp90)
REVERT: D  194 GLU cc_start: 0.8377 (tp30) cc_final: 0.7550 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 103
  average time/residue: 0.0967
  time to fit residues: 14.2705
Evaluate side-chains
  109 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0470
   chunk 43 optimal weight:    0.0070
   chunk 2 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.089356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.068440 restraints weight = 28288.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.070444 restraints weight = 14373.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.071355 restraints weight = 9528.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071691 restraints weight = 8561.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.071615 restraints weight = 7507.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9951  Z= 0.125
  Angle     :  0.564   9.686  13575  Z= 0.292
  Chirality :  0.040   0.161   1515
  Planarity :  0.004   0.066   1682
  Dihedral  :  4.293  53.422   1327
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.44 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.25), residues: 1207
  helix:  2.07 (0.20), residues: 638
  sheet:  0.65 (0.37), residues: 218
  loop : -1.32 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  76 
 TYR   0.009   0.001   TYR A 326 
 PHE   0.021   0.001   PHE B 389 
 TRP   0.012   0.001   TRP D  90 
 HIS   0.005   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9946)
  covalent geometry    : angle       0.56428 (13565)
  SS BOND              : bond        0.00594 (    5)
  SS BOND              : angle       0.70140 (   10)
  hydrogen bonds       : bond        0.05795 (  547)
  hydrogen bonds       : angle       4.07301 ( 1596)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 PRO cc_start: 0.8918 (Cg_endo) cc_final: 0.8680 (Cg_exo)
REVERT: A  112 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8309 (t80)
REVERT: A  253 MET cc_start: 0.8350 (tpp) cc_final: 0.7492 (tmm)
REVERT: A  373 TRP cc_start: 0.7771 (p-90) cc_final: 0.7384 (p-90)
REVERT: B  112 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7574 (t80)
REVERT: B  196 MET cc_start: 0.7838 (tpt) cc_final: 0.7566 (tpp)
REVERT: B  203 GLU cc_start: 0.8569 (tp30) cc_final: 0.8336 (tm-30)
REVERT: B  226 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8956 (tt)
REVERT: C  173 GLN cc_start: 0.8551 (tt0) cc_final: 0.8260 (pp30)
REVERT: D   48 TYR cc_start: 0.8757 (t80) cc_final: 0.8175 (t80)
REVERT: D  166 ASP cc_start: 0.8667 (t70) cc_final: 0.8465 (t70)
REVERT: D  174 MET cc_start: 0.8236 (ttt) cc_final: 0.7645 (tpt)
REVERT: D  183 ASP cc_start: 0.9293 (p0) cc_final: 0.9054 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1035
  time to fit residues: 15.9424
Evaluate side-chains
  108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 PHE
Chi-restraints excluded: chain A residue   67 CYS
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  144 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.086603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.065413 restraints weight = 28658.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.067367 restraints weight = 14487.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068282 restraints weight = 9445.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.068549 restraints weight = 8442.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.068561 restraints weight = 7549.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9951  Z= 0.176
  Angle     :  0.603  12.254  13575  Z= 0.313
  Chirality :  0.041   0.160   1515
  Planarity :  0.005   0.073   1682
  Dihedral  :  4.365  55.739   1327
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.34 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1207
  helix:  1.91 (0.20), residues: 656
  sheet:  0.63 (0.38), residues: 218
  loop : -1.52 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 197 
 TYR   0.014   0.001   TYR D  31 
 PHE   0.023   0.001   PHE B 389 
 TRP   0.011   0.001   TRP D  90 
 HIS   0.004   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 9946)
  covalent geometry    : angle       0.60293 (13565)
  SS BOND              : bond        0.00805 (    5)
  SS BOND              : angle       1.11230 (   10)
  hydrogen bonds       : bond        0.06483 (  547)
  hydrogen bonds       : angle       4.23078 ( 1596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1500.87 seconds
wall clock time: 26 minutes 40.13 seconds (1600.13 seconds total)