Starting phenix.real_space_refine
on Thu Sep 18 17:02:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ofu_70443/09_2025/9ofu_70443.map"
  }
  resolution = 3.9
  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=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      71      5.16       5
     C    6151      2.51       5
     N    1775      2.21       5
     O    1990      1.98       5
     H    8591      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18644
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "E"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 668
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "F"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 685
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "C"
      Number of atoms: 4609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 4609
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 10, 'TRANS': 276}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 4035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 4035
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 11, 'TRANS': 234}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 4640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 4640
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 9, 'TRANS': 279}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 4007
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 10, 'TRANS': 233}
          Chain breaks: 7
  Time building chain proxies: 3.21, per 1000 atoms: 0.17
  Number of scatterers: 18644
  At special positions: 0
  Unit cell: (121.18, 122.01, 116.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      71     16.00
     P      66     15.00
     O    1990      8.00
     N    1775      7.00
     C    6151      6.00
     H    8591      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.59
  Conformation dependent library (CDL) restraints added in 560.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 12 sheets defined
      45.9% alpha, 22.7% beta
      30 base pairs and 54 stacking pairs defined.
    Time for finding SS restraints: 3.11
  Creating SS restraints...
    Processing helix  chain 'C' and resid 3 through 23
    Processing helix  chain 'C' and resid 26 through 31
      removed outlier: 3.910A  pdb=" N   SER C  31 " --> pdb=" O   HIS C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 54
    Processing helix  chain 'C' and resid 65 through 68
    Processing helix  chain 'C' and resid 69 through 75
    Processing helix  chain 'C' and resid 94 through 99
      removed outlier: 4.109A  pdb=" N   TYR C  98 " --> pdb=" O   ASN C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
    Processing helix  chain 'C' and resid 110 through 114
    Processing helix  chain 'C' and resid 120 through 128
    Processing helix  chain 'C' and resid 162 through 166
    Processing helix  chain 'C' and resid 208 through 212
      removed outlier: 3.516A  pdb=" N   ILE C 212 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 242
      removed outlier: 3.690A  pdb=" N   LEU C 241 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 250
      removed outlier: 3.651A  pdb=" N   LEU C 249 " --> pdb=" O   GLU C 245 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU C 250 " --> pdb=" O   PRO C 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 245 through 250'
    Processing helix  chain 'C' and resid 254 through 258
    Processing helix  chain 'C' and resid 259 through 261
      No H-bonds generated for 'chain 'C' and resid 259 through 261'
    Processing helix  chain 'C' and resid 262 through 277
      removed outlier: 3.633A  pdb=" N   LEU C 266 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   MET C 273 " --> pdb=" O   THR C 269 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE C 274 " --> pdb=" O   HIS C 270 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   THR C 275 " --> pdb=" O   HIS C 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 26
      removed outlier: 3.652A  pdb=" N   MET D  25 " --> pdb=" O   GLU D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 53
    Processing helix  chain 'D' and resid 70 through 82
    Processing helix  chain 'D' and resid 102 through 108
    Processing helix  chain 'D' and resid 110 through 115
      removed outlier: 4.131A  pdb=" N   TRP D 114 " --> pdb=" O   PRO D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 123
    Processing helix  chain 'D' and resid 124 through 126
      No H-bonds generated for 'chain 'D' and resid 124 through 126'
    Processing helix  chain 'D' and resid 127 through 135
    Processing helix  chain 'D' and resid 289 through 295
    Processing helix  chain 'D' and resid 297 through 302
      removed outlier: 3.581A  pdb=" N   LEU D 301 " --> pdb=" O   GLN D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 329
      removed outlier: 3.854A  pdb=" N   PHE D 322 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLN D 323 " --> pdb=" O   ARG D 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 23
    Processing helix  chain 'A' and resid 26 through 33
      removed outlier: 3.814A  pdb=" N   HIS A  32 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 54
      removed outlier: 3.732A  pdb=" N   ALA A  54 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 4.301A  pdb=" N   CYS A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 69'
    Processing helix  chain 'A' and resid 69 through 75
      removed outlier: 4.147A  pdb=" N   LYS A  73 " --> pdb=" O   CYS A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 100
      removed outlier: 3.899A  pdb=" N   TYR A  98 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.514A  pdb=" N   LEU A 106 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 119 through 128
    Processing helix  chain 'A' and resid 162 through 166
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.554A  pdb=" N   ILE A 212 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 243
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.862A  pdb=" N   LEU A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 245 through 250'
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 262 through 277
      removed outlier: 3.790A  pdb=" N   LEU A 266 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 37 through 53
    Processing helix  chain 'B' and resid 70 through 82
    Processing helix  chain 'B' and resid 102 through 108
      removed outlier: 3.554A  pdb=" N   VAL B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 115
      removed outlier: 3.821A  pdb=" N   TRP B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 124 through 126
      No H-bonds generated for 'chain 'B' and resid 124 through 126'
    Processing helix  chain 'B' and resid 127 through 134
    Processing helix  chain 'B' and resid 289 through 294
    Processing helix  chain 'B' and resid 305 through 310
      removed outlier: 4.256A  pdb=" N   PHE B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 329
      removed outlier: 3.734A  pdb=" N   VAL B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   VAL B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LYS B 327 " --> pdb=" O   GLN B 323 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 80 through 81
      removed outlier: 3.619A  pdb=" N   VAL C 200 " --> pdb=" O   HIS C 176 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS C 176 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY C 175 " --> pdb=" O   ARG C 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 231 through 234
      removed outlier: 5.899A  pdb=" N   ARG C 224 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   CYS C 234 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU C 222 " --> pdb=" O   CYS C 234 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER C 223 " --> pdb=" O   CYS C 316 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS C 316 " --> pdb=" O   SER C 223 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   GLY C 292 " --> pdb=" O   ALA C 288 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA C 288 " --> pdb=" O   GLY C 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 231 through 234
      removed outlier: 5.899A  pdb=" N   ARG C 224 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   CYS C 234 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU C 222 " --> pdb=" O   CYS C 234 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER C 223 " --> pdb=" O   CYS C 316 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS C 316 " --> pdb=" O   SER C 223 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   CYS C 313 " --> pdb=" O   ILE C 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 96 through 99
      removed outlier: 3.507A  pdb=" N   ALA D 249 " --> pdb=" O   PHE D  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 272 through 275
      removed outlier: 3.664A  pdb=" N   PHE D 273 " --> pdb=" O   ASN D 371 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASN D 371 " --> pdb=" O   PHE D 273 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER D 275 " --> pdb=" O   CYS D 369 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 336 through 337
      removed outlier: 3.713A  pdb=" N   MET D 349 " --> pdb=" O   PHE D 337 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 91
      removed outlier: 6.499A  pdb=" N   MET A  88 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   THR A  83 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR A  90 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS A 203 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   MET A 196 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 200 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 174 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLU A 204 " --> pdb=" O   HIS A 172 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 234
      removed outlier: 6.292A  pdb=" N   ARG A 224 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   CYS A 234 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU A 222 " --> pdb=" O   CYS A 234 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 234
      removed outlier: 6.292A  pdb=" N   ARG A 224 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   CYS A 234 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU A 222 " --> pdb=" O   CYS A 234 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   MET A 286 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87
    Processing sheet with id=AB2, first strand: chain 'B' and resid 285 through 286
      removed outlier: 3.511A  pdb=" N   PHE B 285 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS B 369 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338
      removed outlier: 3.683A  pdb=" N   PHE B 337 " --> pdb=" O   MET B 349 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1062 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      54 stacking parallelities
  Total time for adding SS restraints: 3.80

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 8562
        1.02 -     1.21: 31
        1.21 -     1.41: 4350
        1.41 -     1.61: 5931
        1.61 -     1.81: 113
  Bond restraints: 18987
  Sorted by residual:
  bond pdb=" NE  ARG B 276 "
       pdb=" HE  ARG B 276 "
    ideal  model  delta    sigma   weight residual
    0.860  0.970 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C   THR C 153 "
       pdb=" O   THR C 153 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.38e-02 5.25e+03 5.38e+00
  bond pdb=" C   GLN A 103 "
       pdb=" O   GLN A 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.210  0.027 1.15e-02 7.56e+03 5.35e+00
  bond pdb=" CA  ARG B 276 "
       pdb=" C   ARG B 276 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 1.24e-02 6.50e+03 4.30e+00
  bond pdb=" CA  GLU A 105 "
       pdb=" C   GLU A 105 "
    ideal  model  delta    sigma   weight residual
    1.522  1.493  0.029 1.41e-02 5.03e+03 4.25e+00
  ... (remaining 18982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.03: 33732
        6.03 -    12.07: 3
       12.07 -    18.10: 0
       18.10 -    24.13: 2
       24.13 -    30.17: 4
  Bond angle restraints: 33741
  Sorted by residual:
  angle pdb="HG22 THR A 102 "
        pdb=" CG2 THR A 102 "
        pdb="HG23 THR A 102 "
      ideal   model   delta    sigma   weight residual
     109.00   78.83   30.17 3.00e+00 1.11e-01 1.01e+02
  angle pdb="HG21 THR A 102 "
        pdb=" CG2 THR A 102 "
        pdb="HG22 THR A 102 "
      ideal   model   delta    sigma   weight residual
     109.00   78.92   30.08 3.00e+00 1.11e-01 1.01e+02
  angle pdb=" CB  THR A 102 "
        pdb=" CG2 THR A 102 "
        pdb="HG23 THR A 102 "
      ideal   model   delta    sigma   weight residual
     110.00   81.87   28.13 3.00e+00 1.11e-01 8.79e+01
  angle pdb=" CB  THR A 102 "
        pdb=" CG2 THR A 102 "
        pdb="HG21 THR A 102 "
      ideal   model   delta    sigma   weight residual
     110.00   81.98   28.02 3.00e+00 1.11e-01 8.73e+01
  angle pdb=" CB  THR A 102 "
        pdb=" CG2 THR A 102 "
        pdb="HG22 THR A 102 "
      ideal   model   delta    sigma   weight residual
     110.00  132.45  -22.45 3.00e+00 1.11e-01 5.60e+01
  ... (remaining 33736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.36: 8120
       27.36 -    54.73: 716
       54.73 -    82.09: 101
       82.09 -   109.46: 7
      109.46 -   136.82: 1
  Dihedral angle restraints: 8945
    sinusoidal: 5173
      harmonic: 3772
  Sorted by residual:
  dihedral pdb=" C   THR C  83 "
           pdb=" N   THR C  83 "
           pdb=" CA  THR C  83 "
           pdb=" CB  THR C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.14   10.14     0      2.50e+00 1.60e-01 1.64e+01
  dihedral pdb=" C4'  DC F  52 "
           pdb=" C3'  DC F  52 "
           pdb=" O3'  DC F  52 "
           pdb=" P    DA F  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   83.18  136.82     1      3.50e+01 8.16e-04 1.36e+01
  dihedral pdb=" CA  PRO A 117 "
           pdb=" C   PRO A 117 "
           pdb=" N   CYS A 118 "
           pdb=" CA  CYS A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 8942 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1437
       0.064 -    0.127: 150
       0.127 -    0.191: 10
       0.191 -    0.254: 0
       0.254 -    0.318: 1
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" CA  THR C  83 "
            pdb=" N   THR C  83 "
            pdb=" C   THR C  83 "
            pdb=" CB  THR C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ILE C  91 "
            pdb=" N   ILE C  91 "
            pdb=" C   ILE C  91 "
            pdb=" CB  ILE C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.36e-01
  chirality pdb=" CA  ILE C 202 "
            pdb=" N   ILE C 202 "
            pdb=" C   ILE C 202 "
            pdb=" CB  ILE C 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1595 not shown)

  Planarity restraints: 2579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C 283 "   -0.188 2.00e-02 2.50e+03   4.00e-01 2.41e+03
        pdb=" CD  GLN C 283 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN C 283 "    0.177 2.00e-02 2.50e+03
        pdb=" NE2 GLN C 283 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN C 283 "    0.671 2.00e-02 2.50e+03
        pdb="HE22 GLN C 283 "   -0.667 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 103 "   -0.161 2.00e-02 2.50e+03   1.83e-01 5.03e+02
        pdb=" CD  GLN A 103 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 103 "    0.158 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 103 "   -0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN A 103 "    0.274 2.00e-02 2.50e+03
        pdb="HE22 GLN A 103 "   -0.275 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 299 "   -0.072 2.00e-02 2.50e+03   7.22e-02 7.81e+01
        pdb=" CD  GLN A 299 "    0.021 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 299 "    0.056 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 299 "    0.008 2.00e-02 2.50e+03
        pdb="HE21 GLN A 299 "   -0.112 2.00e-02 2.50e+03
        pdb="HE22 GLN A 299 "    0.099 2.00e-02 2.50e+03
  ... (remaining 2576 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 451
        2.11 -     2.73: 30984
        2.73 -     3.36: 50753
        3.36 -     3.98: 64554
        3.98 -     4.60: 100961
  Nonbonded interactions: 247703
  Sorted by model distance:
  nonbonded pdb=" HE3 MET A  99 "
            pdb=" HB3 MET A 150 "
     model   vdw
     1.490 2.440
  nonbonded pdb=" HB3 LEU A 261 "
            pdb="HH21 ARG A 285 "
     model   vdw
     1.495 2.270
  nonbonded pdb=" HD1 HIS A 259 "
            pdb=" H   LEU A 261 "
     model   vdw
     1.508 2.100
  nonbonded pdb=" HE2 MET A  99 "
            pdb=" HE1 MET A 150 "
     model   vdw
     1.512 2.440
  nonbonded pdb="HG22 VAL C  81 "
            pdb=" HB  ILE C  89 "
     model   vdw
     1.541 2.440
  ... (remaining 247698 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' and (resid 1 through 54 or resid 65 through 129 or resid 141 through  \ 
180 or resid 195 through 324))
  selection = (chain 'C' and (resid 1 through 180 or resid 195 through 212 or resid 218 throug \ 
h 324))
}
ncs_group {
  reference = (chain 'B' and (resid 6 through 177 or resid 210 through 253 or resid 271 throug \ 
h 309 or resid 313 through 373))
  selection = (chain 'D' and (resid 6 through 27 or resid 35 through 88 or resid 93 through 13 \ 
4 or resid 171 through 221 or resid 247 through 253 or resid 271 through 373))
}

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:             4.260
  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:             0.120
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     19.670
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
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      :  0.004   0.036  10396  Z= 0.210
  Angle     :  0.635   7.976  14304  Z= 0.372
  Chirality :  0.040   0.318   1598
  Planarity :  0.004   0.043   1575
  Dihedral  : 20.090 136.820   4005
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.28), residues: 1014
  helix:  1.01 (0.28), residues: 353
  sheet: -2.03 (0.32), residues: 244
  loop : -0.02 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 276 
 TYR   0.018   0.002   TYR C 180 
 PHE   0.014   0.001   PHE D 283 
 TRP   0.031   0.002   TRP D 348 
 HIS   0.007   0.001   HIS C 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (10396)
  covalent geometry    : angle       0.63475 (14304)
  hydrogen bonds       : bond        0.18120 (  449)
  hydrogen bonds       : angle       8.36695 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  145 SER cc_start: 0.7952 (t) cc_final: 0.7558 (m)
REVERT: C  161 MET cc_start: 0.7075 (tpp) cc_final: 0.6862 (tpp)
REVERT: D   49 MET cc_start: 0.7312 (mmm) cc_final: 0.6629 (mmm)
REVERT: A   72 LEU cc_start: 0.6784 (tp) cc_final: 0.6529 (tp)
REVERT: A  310 GLN cc_start: 0.6407 (mm110) cc_final: 0.5587 (pm20)
REVERT: B   23 SER cc_start: 0.8719 (p) cc_final: 0.8276 (m)
REVERT: B   25 MET cc_start: 0.8195 (tpp) cc_final: 0.7992 (tpp)
REVERT: B  274 ILE cc_start: 0.8126 (tp) cc_final: 0.7789 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2091
  time to fit residues: 76.6465
Evaluate side-chains
  193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 HIS
C 270 HIS
A 208 HIS
B 358 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.200943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.164085 restraints weight = 37225.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.167270 restraints weight = 33299.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.168640 restraints weight = 25363.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.169095 restraints weight = 19056.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.169293 restraints weight = 17691.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10396  Z= 0.163
  Angle     :  0.562   5.707  14304  Z= 0.311
  Chirality :  0.039   0.176   1598
  Planarity :  0.004   0.047   1575
  Dihedral  : 21.523 134.834   1862
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.17 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.27), residues: 1014
  helix:  1.20 (0.28), residues: 364
  sheet: -1.91 (0.30), residues: 253
  loop : -0.05 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  40 
 TYR   0.014   0.002   TYR A  90 
 PHE   0.012   0.002   PHE A 221 
 TRP   0.012   0.001   TRP D 348 
 HIS   0.008   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10396)
  covalent geometry    : angle       0.56168 (14304)
  hydrogen bonds       : bond        0.04360 (  449)
  hydrogen bonds       : angle       6.13624 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 ARG cc_start: 0.6573 (mtp-110) cc_final: 0.6348 (mtp180)
REVERT: C  145 SER cc_start: 0.8084 (t) cc_final: 0.7710 (m)
REVERT: C  299 GLN cc_start: 0.8209 (tt0) cc_final: 0.7761 (tm-30)
REVERT: D   99 VAL cc_start: 0.8528 (p) cc_final: 0.8149 (t)
REVERT: D  135 LEU cc_start: 0.6526 (pp) cc_final: 0.6110 (pp)
REVERT: A   72 LEU cc_start: 0.6906 (tp) cc_final: 0.6615 (tp)
REVERT: A   85 ASP cc_start: 0.7462 (t0) cc_final: 0.7200 (t0)
REVERT: B  287 ASP cc_start: 0.7640 (m-30) cc_final: 0.7387 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 215
  average time/residue: 0.2166
  time to fit residues: 64.0454
Evaluate side-chains
  204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 191
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  354 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0770
   chunk 75 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0870
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
C 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.198593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.160471 restraints weight = 37328.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.161372 restraints weight = 33171.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.162926 restraints weight = 28107.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.163190 restraints weight = 24085.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163719 restraints weight = 21164.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10396  Z= 0.151
  Angle     :  0.540   5.412  14304  Z= 0.293
  Chirality :  0.038   0.171   1598
  Planarity :  0.004   0.049   1575
  Dihedral  : 21.329 132.882   1862
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.98 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.28), residues: 1014
  helix:  1.27 (0.28), residues: 371
  sheet: -1.76 (0.30), residues: 253
  loop : -0.31 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 289 
 TYR   0.017   0.001   TYR B 120 
 PHE   0.011   0.001   PHE D 283 
 TRP   0.008   0.001   TRP D 348 
 HIS   0.006   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10396)
  covalent geometry    : angle       0.53956 (14304)
  hydrogen bonds       : bond        0.03726 (  449)
  hydrogen bonds       : angle       5.60660 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  145 SER cc_start: 0.8366 (t) cc_final: 0.7937 (m)
REVERT: C  299 GLN cc_start: 0.8312 (tt0) cc_final: 0.7927 (tm-30)
REVERT: D   99 VAL cc_start: 0.8507 (p) cc_final: 0.8180 (t)
REVERT: D  135 LEU cc_start: 0.6737 (pp) cc_final: 0.6481 (pp)
REVERT: A   72 LEU cc_start: 0.6958 (tp) cc_final: 0.6640 (tp)
REVERT: B   76 HIS cc_start: 0.5490 (t70) cc_final: 0.5229 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 217
  average time/residue: 0.2231
  time to fit residues: 68.5250
Evaluate side-chains
  203 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 270 HIS
B 111 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.189847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.153082 restraints weight = 38365.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.152334 restraints weight = 35493.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.155055 restraints weight = 34755.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.155334 restraints weight = 24132.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.156597 restraints weight = 24682.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10396  Z= 0.194
  Angle     :  0.580   5.977  14304  Z= 0.318
  Chirality :  0.040   0.165   1598
  Planarity :  0.004   0.050   1575
  Dihedral  : 21.356 131.072   1862
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.69 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.27), residues: 1014
  helix:  1.11 (0.28), residues: 364
  sheet: -1.81 (0.30), residues: 246
  loop : -0.69 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 276 
 TYR   0.011   0.001   TYR A 319 
 PHE   0.019   0.002   PHE D 283 
 TRP   0.004   0.001   TRP D 348 
 HIS   0.010   0.001   HIS D 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (10396)
  covalent geometry    : angle       0.58000 (14304)
  hydrogen bonds       : bond        0.03679 (  449)
  hydrogen bonds       : angle       5.47773 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7527 (t)
REVERT: C   88 MET cc_start: 0.8072 (mmm) cc_final: 0.7410 (mtt)
REVERT: C  145 SER cc_start: 0.8537 (t) cc_final: 0.7981 (m)
REVERT: D   99 VAL cc_start: 0.8520 (p) cc_final: 0.8235 (t)
REVERT: D  355 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7098 (p)
REVERT: A   72 LEU cc_start: 0.6842 (tp) cc_final: 0.6609 (tp)
  outliers start: 36
  outliers final: 27
  residues processed: 204
  average time/residue: 0.2220
  time to fit residues: 63.9613
Evaluate side-chains
  200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
C 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.187729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.150010 restraints weight = 38234.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.149537 restraints weight = 37771.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.152566 restraints weight = 32645.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.152663 restraints weight = 23070.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.153251 restraints weight = 24069.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10396  Z= 0.195
  Angle     :  0.576   6.990  14304  Z= 0.315
  Chirality :  0.040   0.165   1598
  Planarity :  0.004   0.054   1575
  Dihedral  : 21.353 127.336   1862
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 21.60 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.27), residues: 1014
  helix:  1.17 (0.28), residues: 356
  sheet: -1.71 (0.32), residues: 231
  loop : -0.93 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 149 
 TYR   0.011   0.001   TYR A 319 
 PHE   0.022   0.002   PHE D 283 
 TRP   0.003   0.001   TRP D 348 
 HIS   0.011   0.001   HIS D 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (10396)
  covalent geometry    : angle       0.57641 (14304)
  hydrogen bonds       : bond        0.03649 (  449)
  hydrogen bonds       : angle       5.44947 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 171
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7600 (t)
REVERT: C   88 MET cc_start: 0.8203 (mmm) cc_final: 0.7406 (mtt)
REVERT: C  122 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7132 (mm-30)
REVERT: C  145 SER cc_start: 0.8509 (t) cc_final: 0.8010 (m)
REVERT: D   99 VAL cc_start: 0.8505 (p) cc_final: 0.8256 (t)
REVERT: A   72 LEU cc_start: 0.6881 (tp) cc_final: 0.6654 (tp)
  outliers start: 40
  outliers final: 31
  residues processed: 192
  average time/residue: 0.2405
  time to fit residues: 63.4908
Evaluate side-chains
  192 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 82 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 225 HIS
C 270 HIS
** A 270 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 = 0.4343 r_free = 0.4343 target = 0.190839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.153618 restraints weight = 37490.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.154163 restraints weight = 38129.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156432 restraints weight = 31396.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.156679 restraints weight = 22572.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.157406 restraints weight = 20669.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  10396  Z= 0.245
  Angle     :  0.617   7.531  14304  Z= 0.343
  Chirality :  0.041   0.161   1598
  Planarity :  0.005   0.056   1575
  Dihedral  : 21.531 122.210   1862
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 22.21 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.26), residues: 1014
  helix:  0.95 (0.28), residues: 355
  sheet: -1.84 (0.32), residues: 230
  loop : -1.37 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 276 
 TYR   0.015   0.002   TYR A 293 
 PHE   0.027   0.002   PHE D 283 
 TRP   0.003   0.001   TRP A 168 
 HIS   0.007   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (10396)
  covalent geometry    : angle       0.61717 (14304)
  hydrogen bonds       : bond        0.04074 (  449)
  hydrogen bonds       : angle       5.66767 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 170
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (t)
REVERT: C   88 MET cc_start: 0.8152 (mmm) cc_final: 0.7327 (mtt)
REVERT: C  122 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7641 (tt0)
REVERT: D   99 VAL cc_start: 0.8460 (p) cc_final: 0.8232 (t)
REVERT: A   72 LEU cc_start: 0.6890 (tp) cc_final: 0.6673 (tp)
REVERT: A  198 CYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8038 (m)
  outliers start: 46
  outliers final: 36
  residues processed: 198
  average time/residue: 0.2244
  time to fit residues: 62.7603
Evaluate side-chains
  197 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  280 GLU
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 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 = 0.4492 r_free = 0.4492 target = 0.204236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.173684 restraints weight = 36529.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.174127 restraints weight = 39692.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.174868 restraints weight = 34159.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.175130 restraints weight = 29454.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.176727 restraints weight = 25977.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10396  Z= 0.134
  Angle     :  0.529   5.748  14304  Z= 0.288
  Chirality :  0.038   0.160   1598
  Planarity :  0.004   0.056   1575
  Dihedral  : 21.364 120.397   1862
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 23.33 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.27), residues: 1014
  helix:  1.42 (0.29), residues: 355
  sheet: -1.89 (0.32), residues: 227
  loop : -1.00 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 149 
 TYR   0.012   0.001   TYR A  90 
 PHE   0.012   0.001   PHE D 283 
 TRP   0.004   0.001   TRP D 346 
 HIS   0.008   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10396)
  covalent geometry    : angle       0.52897 (14304)
  hydrogen bonds       : bond        0.03218 (  449)
  hydrogen bonds       : angle       5.29534 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7444 (t)
REVERT: C  122 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7215 (mm-30)
REVERT: C  145 SER cc_start: 0.8472 (t) cc_final: 0.7991 (m)
REVERT: D   99 VAL cc_start: 0.8156 (p) cc_final: 0.7900 (t)
REVERT: A   72 LEU cc_start: 0.6792 (tp) cc_final: 0.6543 (tp)
REVERT: A  198 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7852 (m)
  outliers start: 35
  outliers final: 23
  residues processed: 184
  average time/residue: 0.2153
  time to fit residues: 56.8084
Evaluate side-chains
  189 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
D 288 HIS
A 270 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.198565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.162197 restraints weight = 36553.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.162388 restraints weight = 35410.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.165695 restraints weight = 30874.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.165549 restraints weight = 21062.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.166003 restraints weight = 22541.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10396  Z= 0.158
  Angle     :  0.537   6.235  14304  Z= 0.293
  Chirality :  0.038   0.160   1598
  Planarity :  0.004   0.057   1575
  Dihedral  : 21.326 115.889   1862
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.53 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.27), residues: 1014
  helix:  1.46 (0.28), residues: 356
  sheet: -1.94 (0.32), residues: 221
  loop : -1.01 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 276 
 TYR   0.016   0.001   TYR D 120 
 PHE   0.017   0.002   PHE D 283 
 TRP   0.004   0.001   TRP D 346 
 HIS   0.011   0.001   HIS D 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10396)
  covalent geometry    : angle       0.53699 (14304)
  hydrogen bonds       : bond        0.03317 (  449)
  hydrogen bonds       : angle       5.25278 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7412 (t)
REVERT: C  122 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7243 (mm-30)
REVERT: C  145 SER cc_start: 0.8513 (t) cc_final: 0.8020 (m)
REVERT: D   99 VAL cc_start: 0.8375 (p) cc_final: 0.8152 (t)
REVERT: A  198 CYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7821 (m)
  outliers start: 37
  outliers final: 30
  residues processed: 184
  average time/residue: 0.2216
  time to fit residues: 57.7929
Evaluate side-chains
  196 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  270 HIS
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  354 PHE
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0970
   chunk 58 optimal weight:    6.9990
   chunk 10 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 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 = 0.4452 r_free = 0.4452 target = 0.200371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.164003 restraints weight = 36613.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.164349 restraints weight = 36126.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.168510 restraints weight = 32266.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.168024 restraints weight = 21728.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.168629 restraints weight = 21548.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.5682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10396  Z= 0.125
  Angle     :  0.514   5.505  14304  Z= 0.280
  Chirality :  0.038   0.161   1598
  Planarity :  0.004   0.056   1575
  Dihedral  : 21.251 112.871   1862
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.34 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.27), residues: 1014
  helix:  1.62 (0.29), residues: 358
  sheet: -1.91 (0.31), residues: 231
  loop : -0.81 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 276 
 TYR   0.008   0.001   TYR A  45 
 PHE   0.013   0.001   PHE D 356 
 TRP   0.004   0.001   TRP D 346 
 HIS   0.010   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10396)
  covalent geometry    : angle       0.51394 (14304)
  hydrogen bonds       : bond        0.03044 (  449)
  hydrogen bonds       : angle       5.12381 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    3 ASP cc_start: 0.7240 (m-30) cc_final: 0.6820 (t70)
REVERT: C   42 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7363 (t)
REVERT: C  145 SER cc_start: 0.8467 (t) cc_final: 0.8014 (m)
REVERT: D   99 VAL cc_start: 0.8347 (p) cc_final: 0.8136 (t)
REVERT: A  198 CYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7744 (m)
  outliers start: 28
  outliers final: 22
  residues processed: 182
  average time/residue: 0.2143
  time to fit residues: 55.8464
Evaluate side-chains
  188 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 270 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.198568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.159835 restraints weight = 36595.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.161988 restraints weight = 35564.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.164044 restraints weight = 28611.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.164561 restraints weight = 20855.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.165022 restraints weight = 18781.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.5862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10396  Z= 0.152
  Angle     :  0.533   6.430  14304  Z= 0.289
  Chirality :  0.038   0.161   1598
  Planarity :  0.004   0.057   1575
  Dihedral  : 21.240 106.466   1862
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.14 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.27), residues: 1014
  helix:  1.61 (0.28), residues: 358
  sheet: -1.83 (0.32), residues: 221
  loop : -0.96 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 149 
 TYR   0.010   0.001   TYR D 120 
 PHE   0.018   0.002   PHE D 356 
 TRP   0.004   0.001   TRP D 346 
 HIS   0.010   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10396)
  covalent geometry    : angle       0.53267 (14304)
  hydrogen bonds       : bond        0.03259 (  449)
  hydrogen bonds       : angle       5.11577 ( 1216)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7408 (t)
REVERT: C  145 SER cc_start: 0.8492 (t) cc_final: 0.7992 (m)
REVERT: D   99 VAL cc_start: 0.8358 (p) cc_final: 0.8144 (t)
REVERT: A  198 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7792 (m)
  outliers start: 31
  outliers final: 26
  residues processed: 185
  average time/residue: 0.2125
  time to fit residues: 56.1475
Evaluate side-chains
  193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  263 SER
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  354 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  270 HIS
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain B residue  355 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   chunk 92 optimal weight:    0.0370
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 96 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 270 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.200913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.164573 restraints weight = 36553.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.165032 restraints weight = 34674.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.168336 restraints weight = 29911.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.168352 restraints weight = 20860.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.168748 restraints weight = 19583.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10396  Z= 0.115
  Angle     :  0.509   5.231  14304  Z= 0.275
  Chirality :  0.038   0.158   1598
  Planarity :  0.004   0.056   1575
  Dihedral  : 21.180 102.226   1862
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 24.95 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.27), residues: 1014
  helix:  1.69 (0.28), residues: 358
  sheet: -1.86 (0.31), residues: 233
  loop : -0.74 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 149 
 TYR   0.009   0.001   TYR A  90 
 PHE   0.014   0.001   PHE D 356 
 TRP   0.009   0.001   TRP D 348 
 HIS   0.017   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10396)
  covalent geometry    : angle       0.50857 (14304)
  hydrogen bonds       : bond        0.02988 (  449)
  hydrogen bonds       : angle       4.99813 ( 1216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3274.15 seconds
wall clock time: 56 minutes 49.92 seconds (3409.92 seconds total)