Starting phenix.real_space_refine
on Fri Jul 25 12:52:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ww2_21927/07_2025/6ww2_21927.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4857      2.51       5
     N    1273      2.21       5
     O    1432      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7594
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1682
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "K"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 921
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1624
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "R"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3367
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 5.33, per 1000 atoms: 0.70
  Number of scatterers: 7594
  At special positions: 0
  Unit cell: (112.112, 146.608, 98.098, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1432      8.00
     N    1273      7.00
     C    4857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.02
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 222 " - pdb=" SG  CYS R 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 315 " - pdb=" SG  CYS R 390 " distance=2.03

  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: 1.85
  Conformation dependent library (CDL) restraints added in 953.0 milliseconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      38.8% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'H' and resid 65 through 68
      removed outlier: 3.667A  pdb=" N   LYS H  68 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 65 through 68'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.945A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.659A  pdb=" N   TRP H 111 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 202 through 206
      removed outlier: 3.703A  pdb=" N   GLN H 206 " --> pdb=" O   LEU H 203 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 3.967A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 94 through 98
      removed outlier: 3.735A  pdb=" N   LEU L  97 " --> pdb=" O   TYR L  94 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL L  98 " --> pdb=" O   TYR L  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 94 through 98'
    Processing helix  chain 'L' and resid 185 through 189
      removed outlier: 4.252A  pdb=" N   GLU L 189 " --> pdb=" O   LYS L 185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 185 through 189'
    Processing helix  chain 'R' and resid 211 through 215
      removed outlier: 3.566A  pdb=" N   GLN R 214 " --> pdb=" O   ARG R 211 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL R 215 " --> pdb=" O   THR R 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 211 through 215'
    Processing helix  chain 'R' and resid 228 through 230
      No H-bonds generated for 'chain 'R' and resid 228 through 230'
    Processing helix  chain 'R' and resid 231 through 261
      removed outlier: 4.704A  pdb=" N   PHE R 237 " --> pdb=" O   THR R 233 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE R 239 " --> pdb=" O   ALA R 235 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   GLY R 240 " --> pdb=" O   THR R 236 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TRP R 242 " --> pdb=" O   TRP R 238 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU R 245 " --> pdb=" O   LEU R 241 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR R 250 " --> pdb=" O   CYS R 246 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR R 252 " --> pdb=" O   ILE R 248 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR R 253 " --> pdb=" O   SER R 249 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL R 254 " --> pdb=" O   THR R 250 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA R 255 " --> pdb=" O   SER R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 267
      No H-bonds generated for 'chain 'R' and resid 265 through 267'
    Processing helix  chain 'R' and resid 268 through 292
      removed outlier: 4.188A  pdb=" N   ILE R 272 " --> pdb=" O   GLU R 268 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE R 273 " --> pdb=" O   ARG R 269 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU R 279 " --> pdb=" O   SER R 275 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   CYS R 280 " --> pdb=" O   ALA R 276 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE R 285 " --> pdb=" O   VAL R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 297
      removed outlier: 3.679A  pdb=" N   VAL R 296 " --> pdb=" O   GLY R 292 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA R 297 " --> pdb=" O   HIS R 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 292 through 297'
    Processing helix  chain 'R' and resid 314 through 345
      removed outlier: 4.028A  pdb=" N   VAL R 318 " --> pdb=" O   LEU R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 349 through 379
      removed outlier: 3.627A  pdb=" N   TYR R 356 " --> pdb=" O   ALA R 352 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR R 359 " --> pdb=" O   GLY R 355 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   LEU R 362 " --> pdb=" O   GLN R 358 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TRP R 365 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU R 366 " --> pdb=" O   LEU R 362 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE R 367 " --> pdb=" O   ALA R 363 " (cutoff:3.500A)
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'R' and resid 396 through 404
    Processing helix  chain 'R' and resid 404 through 1025
      removed outlier: 3.831A  pdb=" N   LEU R 408 " --> pdb=" O   VAL R 404 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL R 409 " --> pdb=" O   LEU R 405 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU R 412 " --> pdb=" O   LEU R 408 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE R 418 " --> pdb=" O   VAL R 414 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASN R1018 " --> pdb=" O   THR R1014 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1029 through 1049
      removed outlier: 4.204A  pdb=" N   LYS R1037 " --> pdb=" O   ASP R1033 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA R1048 " --> pdb=" O   ASP R1044 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1064 through 1086
      removed outlier: 4.640A  pdb=" N   PHE R1070 " --> pdb=" O   PHE R1066 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LYS R1082 " --> pdb=" O   ASP R1078 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU R1083 " --> pdb=" O   ASP R1079 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA R1084 " --> pdb=" O   ALA R1080 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1089 through 1098
    Processing helix  chain 'R' and resid 1098 through 1106
      removed outlier: 4.523A  pdb=" N   THR R1102 " --> pdb=" O   GLN R1098 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR R1106 " --> pdb=" O   THR R1102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1106 through 479
      removed outlier: 3.804A  pdb=" N   ARG R1113 " --> pdb=" O   LYS R1109 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R1118 " --> pdb=" O   ALA R1114 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU R 446 " --> pdb=" O   LYS R 442 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE R 448 " --> pdb=" O   GLU R 444 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   ARG R 449 " --> pdb=" O   LYS R 445 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE R 453 " --> pdb=" O   ARG R 449 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR R 454 " --> pdb=" O   ILE R 450 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL R 459 " --> pdb=" O   LEU R 455 " (cutoff:3.500A)
      Proline residue:  R 460  - end of helix
      removed outlier: 3.919A  pdb=" N   HIS R 473 " --> pdb=" O   LEU R 469 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 500 through 511
      removed outlier: 3.805A  pdb=" N   LYS R 506 " --> pdb=" O   VAL R 502 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR R 507 " --> pdb=" O   LEU R 503 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   PHE R 508 " --> pdb=" O   MET R 504 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU R 511 " --> pdb=" O   TYR R 507 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 511 through 520
      removed outlier: 4.257A  pdb=" N   ILE R 515 " --> pdb=" O   LEU R 511 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR R 516 " --> pdb=" O   VAL R 512 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 523 through 536
      removed outlier: 4.233A  pdb=" N   ARG R 536 " --> pdb=" O   ARG R 532 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15
      removed outlier: 3.705A  pdb=" N   ALA H  52 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR H  53 " --> pdb=" O   SER H  62 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.068A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.068A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168
      removed outlier: 3.597A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6
      removed outlier: 3.738A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER K  25 " --> pdb=" O   GLN K   3 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY K  16 " --> pdb=" O   SER K  85 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   SER K  85 " --> pdb=" O   GLY K  16 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 11 through 12
      removed outlier: 6.466A  pdb=" N   VAL K  12 " --> pdb=" O   GLN K 116 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   THR K 118 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL K 117 " --> pdb=" O   ALA K  92 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.927A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120
      removed outlier: 6.189A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 147
      removed outlier: 3.877A  pdb=" N   ALA L 195 " --> pdb=" O   LYS L 151 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 147
    Processing sheet with id=AB4, first strand: chain 'R' and resid 381 through 383

    381 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2228
        1.34 -     1.46: 2136
        1.46 -     1.59: 3373
        1.59 -     1.71: 0
        1.71 -     1.83: 44
  Bond restraints: 7781
  Sorted by residual:
  bond pdb=" CB  TRP H 102 "
       pdb=" CG  TRP H 102 "
    ideal  model  delta    sigma   weight residual
    1.498  1.420  0.078 3.10e-02 1.04e+03 6.30e+00
  bond pdb=" C   VAL R 459 "
       pdb=" N   PRO R 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.369 -0.034 1.36e-02 5.41e+03 6.12e+00
  bond pdb=" CB  TRP R 242 "
       pdb=" CG  TRP R 242 "
    ideal  model  delta    sigma   weight residual
    1.498  1.427  0.071 3.10e-02 1.04e+03 5.30e+00
  bond pdb=" CB  PHE H 180 "
       pdb=" CG  PHE H 180 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.36e+00
  bond pdb=" CB  VAL R 215 "
       pdb=" CG2 VAL R 215 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.31e+00
  ... (remaining 7776 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 9956
        2.06 -     4.12: 536
        4.12 -     6.19: 70
        6.19 -     8.25: 25
        8.25 -    10.31: 3
  Bond angle restraints: 10590
  Sorted by residual:
  angle pdb=" C   GLU R 202 "
        pdb=" N   SER R 203 "
        pdb=" CA  SER R 203 "
      ideal   model   delta    sigma   weight residual
     121.54  130.77   -9.23 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" C   PHE R 196 "
        pdb=" N   VAL R 197 "
        pdb=" CA  VAL R 197 "
      ideal   model   delta    sigma   weight residual
     122.13  129.76   -7.63 1.85e+00 2.92e-01 1.70e+01
  angle pdb=" C   MET R 261 "
        pdb=" N   GLU R 262 "
        pdb=" CA  GLU R 262 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   ALA R1048 "
        pdb=" N   THR R1049 "
        pdb=" CA  THR R1049 "
      ideal   model   delta    sigma   weight residual
     121.70  128.66   -6.96 1.80e+00 3.09e-01 1.50e+01
  angle pdb=" C   SER H 217 "
        pdb=" N   ASN H 218 "
        pdb=" CA  ASN H 218 "
      ideal   model   delta    sigma   weight residual
     121.54  128.92   -7.38 1.91e+00 2.74e-01 1.49e+01
  ... (remaining 10585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4139
       17.84 -    35.67: 352
       35.67 -    53.51: 65
       53.51 -    71.35: 9
       71.35 -    89.18: 7
  Dihedral angle restraints: 4572
    sinusoidal: 1720
      harmonic: 2852
  Sorted by residual:
  dihedral pdb=" CA  PRO H 199 "
           pdb=" C   PRO H 199 "
           pdb=" N   SER H 200 "
           pdb=" CA  SER H 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.94   23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  THR R 252 "
           pdb=" C   THR R 252 "
           pdb=" N   THR R 253 "
           pdb=" CA  THR R 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.35  -22.65     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  ASN R 217 "
           pdb=" C   ASN R 217 "
           pdb=" N   CYS R 218 "
           pdb=" CA  CYS R 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.48   21.52     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 4569 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 722
       0.046 -    0.092: 305
       0.092 -    0.137: 115
       0.137 -    0.183: 35
       0.183 -    0.229: 13
  Chirality restraints: 1190
  Sorted by residual:
  chirality pdb=" CB  VAL R 197 "
            pdb=" CA  VAL R 197 "
            pdb=" CG1 VAL R 197 "
            pdb=" CG2 VAL R 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CG  LEU H  89 "
            pdb=" CB  LEU H  89 "
            pdb=" CD1 LEU H  89 "
            pdb=" CD2 LEU H  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  ILE K  98 "
            pdb=" CA  ILE K  98 "
            pdb=" CG1 ILE K  98 "
            pdb=" CG2 ILE K  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1187 not shown)

  Planarity restraints: 1334
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 215 "   -0.046 5.00e-02 4.00e+02   6.81e-02 7.42e+00
        pdb=" N   PRO H 216 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO H 216 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 216 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU R 194 "   -0.042 5.00e-02 4.00e+02   6.37e-02 6.48e+00
        pdb=" N   PRO R 195 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO R 195 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 195 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 238 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   TRP R 238 "    0.043 2.00e-02 2.50e+03
        pdb=" O   TRP R 238 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R 239 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1331 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1672
        2.77 -     3.30: 7298
        3.30 -     3.84: 12541
        3.84 -     4.37: 13931
        4.37 -     4.90: 23896
  Nonbonded interactions: 59338
  Sorted by model distance:
  nonbonded pdb=" O   GLN K   3 "
            pdb=" OG  SER K  25 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   VAL R 513 "
            pdb=" OG1 THR R 516 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   TYR L 188 "
            pdb=" OH  TYR L 194 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   SER H 142 "
            pdb=" OG  SER H 146 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE1 GLU R 308 "
            pdb=" OG  SER R 379 "
     model   vdw
     2.281 3.040
  ... (remaining 59333 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.430
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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      :  0.010   0.088   7788  Z= 0.425
  Angle     :  1.080  10.309  10604  Z= 0.591
  Chirality :  0.062   0.229   1190
  Planarity :  0.008   0.068   1334
  Dihedral  : 14.271  89.182   2723
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.31 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.26), residues: 970
  helix: -1.13 (0.26), residues: 312
  sheet: -0.83 (0.34), residues: 238
  loop : -2.25 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP H 102 
 HIS   0.006   0.002   HIS R 306 
 PHE   0.026   0.004   PHE R 325 
 TYR   0.036   0.003   TYR H  53 
 ARG   0.008   0.001   ARG L 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12880 (  366)
  hydrogen bonds       : angle       6.99717 ( 1065)
  SS BOND              : bond        0.00397 (    7)
  SS BOND              : angle       2.37986 (   14)
  covalent geometry    : bond        0.00967 ( 7781)
  covalent geometry    : angle       1.07681 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: R  411 TYR cc_start: 0.8736 (m-10) cc_final: 0.8286 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1934
  time to fit residues: 18.9631
Evaluate side-chains
  49 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    0.2980
   chunk 73 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.073466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.058500 restraints weight = 33815.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.060014 restraints weight = 19261.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.060973 restraints weight = 13355.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7788  Z= 0.160
  Angle     :  0.669   7.311  10604  Z= 0.357
  Chirality :  0.044   0.199   1190
  Planarity :  0.005   0.057   1334
  Dihedral  :  5.942  24.513   1067
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.20 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.27), residues: 970
  helix: -0.36 (0.28), residues: 320
  sheet: -0.83 (0.33), residues: 246
  loop : -2.08 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 333 
 HIS   0.008   0.001   HIS R 204 
 PHE   0.016   0.002   PHE R 319 
 TYR   0.020   0.002   TYR K  32 
 ARG   0.002   0.000   ARG K  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04392 (  366)
  hydrogen bonds       : angle       5.51716 ( 1065)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       1.17630 (   14)
  covalent geometry    : bond        0.00346 ( 7781)
  covalent geometry    : angle       0.66810 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7414 (m-10) cc_final: 0.7010 (m-10)
REVERT: L  163 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7261 (pp20)
REVERT: R  411 TYR cc_start: 0.8818 (m-10) cc_final: 0.8491 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 62
  average time/residue: 0.1801
  time to fit residues: 16.3240
Evaluate side-chains
  53 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue  462 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.073306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.058254 restraints weight = 34519.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059762 restraints weight = 19646.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.060724 restraints weight = 13669.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7788  Z= 0.157
  Angle     :  0.623   7.094  10604  Z= 0.328
  Chirality :  0.042   0.154   1190
  Planarity :  0.004   0.044   1334
  Dihedral  :  5.438  26.312   1067
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.70 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.27), residues: 970
  helix: -0.05 (0.29), residues: 320
  sheet: -0.71 (0.33), residues: 241
  loop : -2.00 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H 178 
 PHE   0.015   0.001   PHE R 319 
 TYR   0.019   0.002   TYR K  32 
 ARG   0.007   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  366)
  hydrogen bonds       : angle       5.13430 ( 1065)
  SS BOND              : bond        0.00212 (    7)
  SS BOND              : angle       0.96224 (   14)
  covalent geometry    : bond        0.00345 ( 7781)
  covalent geometry    : angle       0.62225 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7402 (m-10) cc_final: 0.7010 (m-10)
REVERT: L    5 MET cc_start: 0.8579 (tpp) cc_final: 0.7910 (tpp)
REVERT: R  411 TYR cc_start: 0.8817 (m-10) cc_final: 0.8330 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 62
  average time/residue: 0.1561
  time to fit residues: 14.7189
Evaluate side-chains
  55 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  315 CYS
Chi-restraints excluded: chain R residue  462 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.058053 restraints weight = 33753.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.059325 restraints weight = 19092.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.060720 restraints weight = 13272.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7788  Z= 0.207
  Angle     :  0.645   7.032  10604  Z= 0.342
  Chirality :  0.043   0.162   1190
  Planarity :  0.004   0.035   1334
  Dihedral  :  5.420  27.960   1067
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.29 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.27), residues: 970
  helix:  0.02 (0.28), residues: 320
  sheet: -0.59 (0.33), residues: 236
  loop : -1.99 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 333 
 HIS   0.003   0.001   HIS R 306 
 PHE   0.015   0.002   PHE R 319 
 TYR   0.014   0.002   TYR K  32 
 ARG   0.006   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  366)
  hydrogen bonds       : angle       5.12284 ( 1065)
  SS BOND              : bond        0.00253 (    7)
  SS BOND              : angle       0.99414 (   14)
  covalent geometry    : bond        0.00462 ( 7781)
  covalent geometry    : angle       0.64430 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.879 
Fit side-chains
REVERT: K   43 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.6147 (pttp)
REVERT: R  306 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6802 (m90)
REVERT: R  411 TYR cc_start: 0.8782 (m-10) cc_final: 0.8276 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1627
  time to fit residues: 14.8589
Evaluate side-chains
  56 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue  508 PHE
Chi-restraints excluded: chain R residue  513 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 83 optimal weight:    0.3980
   chunk 46 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   overall best weight:    1.3782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.073144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.058360 restraints weight = 33952.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.059574 restraints weight = 19846.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.060716 restraints weight = 14338.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7788  Z= 0.148
  Angle     :  0.608   6.868  10604  Z= 0.318
  Chirality :  0.042   0.158   1190
  Planarity :  0.004   0.034   1334
  Dihedral  :  5.145  27.155   1067
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.85 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.27), residues: 970
  helix:  0.19 (0.29), residues: 320
  sheet: -0.57 (0.33), residues: 241
  loop : -1.97 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 333 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE R 319 
 TYR   0.012   0.001   TYR K  32 
 ARG   0.004   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  366)
  hydrogen bonds       : angle       4.93860 ( 1065)
  SS BOND              : bond        0.00185 (    7)
  SS BOND              : angle       0.77209 (   14)
  covalent geometry    : bond        0.00327 ( 7781)
  covalent geometry    : angle       0.60800 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7362 (m-10) cc_final: 0.6997 (m-10)
REVERT: R  306 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.6758 (m90)
REVERT: R  411 TYR cc_start: 0.8731 (m-10) cc_final: 0.8223 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 62
  average time/residue: 0.1613
  time to fit residues: 16.1016
Evaluate side-chains
  59 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.074125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.059615 restraints weight = 33700.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.060917 restraints weight = 18875.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.062183 restraints weight = 13437.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7788  Z= 0.119
  Angle     :  0.587   7.251  10604  Z= 0.303
  Chirality :  0.041   0.152   1190
  Planarity :  0.004   0.034   1334
  Dihedral  :  4.813  25.510   1067
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.73 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.27), residues: 970
  helix:  0.33 (0.29), residues: 319
  sheet: -0.33 (0.33), residues: 245
  loop : -1.95 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.014   0.001   PHE R 319 
 TYR   0.013   0.001   TYR H  83 
 ARG   0.004   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03416 (  366)
  hydrogen bonds       : angle       4.68769 ( 1065)
  SS BOND              : bond        0.00147 (    7)
  SS BOND              : angle       0.73016 (   14)
  covalent geometry    : bond        0.00258 ( 7781)
  covalent geometry    : angle       0.58673 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7266 (m-10) cc_final: 0.6961 (m-10)
REVERT: K   83 MET cc_start: 0.7498 (ttm) cc_final: 0.7088 (ttp)
REVERT: L    5 MET cc_start: 0.8501 (tpp) cc_final: 0.7706 (tpp)
REVERT: R  306 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.6808 (m90)
REVERT: R  411 TYR cc_start: 0.8724 (m-10) cc_final: 0.8284 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1453
  time to fit residues: 15.3188
Evaluate side-chains
  60 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  465 VAL
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.073511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.058256 restraints weight = 33752.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.059754 restraints weight = 19423.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.060743 restraints weight = 13598.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7788  Z= 0.146
  Angle     :  0.603   6.830  10604  Z= 0.312
  Chirality :  0.042   0.156   1190
  Planarity :  0.004   0.068   1334
  Dihedral  :  4.821  24.946   1067
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.46 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.27), residues: 970
  helix:  0.43 (0.29), residues: 313
  sheet: -0.40 (0.33), residues: 247
  loop : -1.81 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.013   0.001   PHE R 319 
 TYR   0.012   0.001   TYR H 116 
 ARG   0.003   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (  366)
  hydrogen bonds       : angle       4.68140 ( 1065)
  SS BOND              : bond        0.00210 (    7)
  SS BOND              : angle       0.85833 (   14)
  covalent geometry    : bond        0.00324 ( 7781)
  covalent geometry    : angle       0.60305 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7410 (m-10) cc_final: 0.7012 (m-10)
REVERT: K   83 MET cc_start: 0.7629 (ttm) cc_final: 0.7134 (ttp)
REVERT: L    5 MET cc_start: 0.8534 (tpp) cc_final: 0.7896 (tpp)
REVERT: R  306 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.6895 (m90)
REVERT: R  411 TYR cc_start: 0.8785 (m-10) cc_final: 0.8263 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 66
  average time/residue: 0.2570
  time to fit residues: 26.1614
Evaluate side-chains
  64 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  390 CYS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  465 VAL
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 62 optimal weight:    0.3980
   chunk 32 optimal weight:    0.4980
   chunk 43 optimal weight:    0.4980
   chunk 66 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.074413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.059131 restraints weight = 34207.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.060655 restraints weight = 19563.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.061617 restraints weight = 13644.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7788  Z= 0.120
  Angle     :  0.599   7.149  10604  Z= 0.308
  Chirality :  0.042   0.170   1190
  Planarity :  0.004   0.057   1334
  Dihedral  :  4.654  23.183   1067
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.83 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.28), residues: 970
  helix:  0.49 (0.29), residues: 314
  sheet: -0.14 (0.34), residues: 243
  loop : -1.79 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.013   0.001   PHE R 319 
 TYR   0.013   0.001   TYR R 278 
 ARG   0.003   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  366)
  hydrogen bonds       : angle       4.59692 ( 1065)
  SS BOND              : bond        0.00162 (    7)
  SS BOND              : angle       0.78029 (   14)
  covalent geometry    : bond        0.00262 ( 7781)
  covalent geometry    : angle       0.59856 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7362 (m-10) cc_final: 0.6983 (m-10)
REVERT: K   83 MET cc_start: 0.7603 (ttm) cc_final: 0.7112 (ttp)
REVERT: L    5 MET cc_start: 0.8476 (tpp) cc_final: 0.7850 (tpp)
REVERT: L  163 GLU cc_start: 0.7557 (pp20) cc_final: 0.7120 (pp20)
REVERT: R  306 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.6879 (m90)
REVERT: R  346 MET cc_start: 0.9275 (mpp) cc_final: 0.8725 (pmm)
REVERT: R  411 TYR cc_start: 0.8779 (m-10) cc_final: 0.8225 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 64
  average time/residue: 0.1529
  time to fit residues: 14.8026
Evaluate side-chains
  63 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  390 CYS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  465 VAL
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.074489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.059339 restraints weight = 34164.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060869 restraints weight = 19422.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061868 restraints weight = 13492.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7788  Z= 0.116
  Angle     :  0.592   7.726  10604  Z= 0.303
  Chirality :  0.041   0.151   1190
  Planarity :  0.004   0.054   1334
  Dihedral  :  4.521  21.674   1067
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.32 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.28), residues: 970
  helix:  0.61 (0.29), residues: 313
  sheet: -0.07 (0.34), residues: 243
  loop : -1.74 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.013   0.001   PHE R 319 
 TYR   0.013   0.001   TYR H  83 
 ARG   0.003   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  366)
  hydrogen bonds       : angle       4.50132 ( 1065)
  SS BOND              : bond        0.00164 (    7)
  SS BOND              : angle       0.75902 (   14)
  covalent geometry    : bond        0.00251 ( 7781)
  covalent geometry    : angle       0.59219 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7369 (m-10) cc_final: 0.6991 (m-10)
REVERT: K   83 MET cc_start: 0.7587 (ttm) cc_final: 0.7111 (ttp)
REVERT: L    5 MET cc_start: 0.8447 (tpp) cc_final: 0.7844 (tpp)
REVERT: L  163 GLU cc_start: 0.7559 (pp20) cc_final: 0.7143 (pp20)
REVERT: R  306 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.6922 (m90)
REVERT: R  346 MET cc_start: 0.9276 (mpp) cc_final: 0.8739 (pmm)
REVERT: R  411 TYR cc_start: 0.8786 (m-10) cc_final: 0.8241 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1523
  time to fit residues: 15.4257
Evaluate side-chains
  61 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  390 CYS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0030
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.074812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061150 restraints weight = 34993.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.062316 restraints weight = 23777.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.062638 restraints weight = 18095.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7788  Z= 0.119
  Angle     :  0.593   7.400  10604  Z= 0.304
  Chirality :  0.041   0.155   1190
  Planarity :  0.004   0.054   1334
  Dihedral  :  4.473  20.653   1067
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 18.93 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.28), residues: 970
  helix:  0.61 (0.29), residues: 315
  sheet: -0.05 (0.34), residues: 242
  loop : -1.73 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.013   0.001   PHE R 319 
 TYR   0.012   0.001   TYR H  83 
 ARG   0.003   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  366)
  hydrogen bonds       : angle       4.48785 ( 1065)
  SS BOND              : bond        0.00158 (    7)
  SS BOND              : angle       0.78348 (   14)
  covalent geometry    : bond        0.00261 ( 7781)
  covalent geometry    : angle       0.59279 (10590)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: H  208 TYR cc_start: 0.7420 (m-10) cc_final: 0.7019 (m-10)
REVERT: K   83 MET cc_start: 0.7442 (ttm) cc_final: 0.7025 (ttp)
REVERT: L    5 MET cc_start: 0.8429 (tpp) cc_final: 0.7771 (tpp)
REVERT: L  163 GLU cc_start: 0.7445 (pp20) cc_final: 0.7088 (pp20)
REVERT: R  306 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.6878 (m90)
REVERT: R  346 MET cc_start: 0.9173 (mpp) cc_final: 0.8736 (pmm)
REVERT: R  411 TYR cc_start: 0.8692 (m-10) cc_final: 0.8207 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1537
  time to fit residues: 14.6474
Evaluate side-chains
  58 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 LEU
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  306 HIS
Chi-restraints excluded: chain R residue  409 VAL
Chi-restraints excluded: chain R residue 1049 THR
Chi-restraints excluded: chain R residue  462 SER
Chi-restraints excluded: chain R residue  508 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 92 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.073973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.058687 restraints weight = 35023.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.060232 restraints weight = 20006.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.061247 restraints weight = 13973.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7788  Z= 0.145
  Angle     :  0.606   7.226  10604  Z= 0.312
  Chirality :  0.042   0.151   1190
  Planarity :  0.004   0.052   1334
  Dihedral  :  4.572  20.928   1067
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.53 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.05 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.28), residues: 970
  helix:  0.68 (0.29), residues: 314
  sheet: -0.06 (0.34), residues: 242
  loop : -1.74 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 333 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.013   0.001   PHE R 319 
 TYR   0.012   0.001   TYR H 116 
 ARG   0.003   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  366)
  hydrogen bonds       : angle       4.54145 ( 1065)
  SS BOND              : bond        0.00189 (    7)
  SS BOND              : angle       0.83017 (   14)
  covalent geometry    : bond        0.00323 ( 7781)
  covalent geometry    : angle       0.60551 (10590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2693.46 seconds
wall clock time: 48 minutes 38.66 seconds (2918.66 seconds total)