Starting phenix.real_space_refine
on Mon Mar 18 20:27:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwc_16282/03_2024/8bwc_16282.pdb"
  }
  resolution = 3.5
  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=  -0.013 sd=   0.031
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7100      2.51       5
     N    1917      2.21       5
     O    2217      1.98       5
     H   10846      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 22112
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 706, 10923
          Classifications: {'peptide': 706}
          Link IDs: {'PTRANS': 27, 'TRANS': 678}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 5445
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 11, 'TRANS': 354}
    Chain: "C"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 933
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 7, 'TRANS': 57}
    Chain: "D"
      Number of atoms: 3460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3460
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 1351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 1351
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
  Time building chain proxies: 9.87, per 1000 atoms: 0.45
  Number of scatterers: 22112
  At special positions: 0
  Unit cell: (114.7, 126.54, 138.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2217      8.00
     N    1917      7.00
     C    7100      6.00
     H   10846      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  - 3.50
        Amino acid           : False - 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: 17.65
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2634

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 17 sheets defined
      24.6% alpha, 28.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.618A  pdb=" N   SER A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 141
      removed outlier: 3.705A  pdb=" N   TYR A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.887A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 3.796A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 221 " --> pdb=" O   GLN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.851A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 367
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.503A  pdb=" N   LYS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 452
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 4.077A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
      removed outlier: 3.613A  pdb=" N   ALA A 730 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ASN A 731 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 44
      removed outlier: 3.569A  pdb=" N   ALA C  44 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 63
      removed outlier: 3.743A  pdb=" N   GLY C  63 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.608A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 65 through 68
    Processing helix  chain 'D' and resid 69 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 119
      removed outlier: 3.672A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 128
    Processing helix  chain 'D' and resid 131 through 135
      removed outlier: 4.405A  pdb=" N   ASP D 134 " --> pdb=" O   ASP D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.875A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS D 176 " --> pdb=" O   ASP D 172 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.630A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
      removed outlier: 3.515A  pdb=" N   GLU D 219 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   MET D 225 " --> pdb=" O   ALA D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 4.398A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL D 234 " --> pdb=" O   GLN D 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 46
      removed outlier: 3.768A  pdb=" N   ILE E  46 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.511A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183
      removed outlier: 6.304A  pdb=" N   GLU A 176 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   VAL A 256 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   GLN A 178 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 12.788A  pdb=" N   VAL A 258 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 9.991A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 12.008A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 9.607A  pdb=" N   ILE A 182 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER B 193 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276
      removed outlier: 6.055A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.297A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.397A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ARG A 338 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 355
      removed outlier: 7.565A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.507A  pdb=" N   GLN A 441 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.513A  pdb=" N   PHE A 440 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 490 " --> pdb=" O   GLY A 510 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG A 526 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 575 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY A 597 " --> pdb=" O   TYR A 574 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 633 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 51
      removed outlier: 5.171A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   SER B 389 " --> pdb=" O   TRP B  48 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.628A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100
      removed outlier: 3.511A  pdb=" N   GLU B  99 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.660A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 157
      removed outlier: 4.045A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.936A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.566A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.744A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 6.580A  pdb=" N   LEU B 346 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLN B 359 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   TRP B 348 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 4.176A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    474 hydrogen bonds defined for protein.
    1284 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: 8.09

  Time building geometry restraints manager: 18.42 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10843
        1.03 -     1.23: 29
        1.23 -     1.42: 4962
        1.42 -     1.62: 6467
        1.62 -     1.81: 61
  Bond restraints: 22362
  Sorted by residual:
  bond pdb=" N   TYR E  28 "
       pdb=" CA  TYR E  28 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.041 1.16e-02 7.43e+03 1.24e+01
  bond pdb=" N   VAL B 357 "
       pdb=" CA  VAL B 357 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.23e-02 6.61e+03 9.43e+00
  bond pdb=" N   VAL B 362 "
       pdb=" CA  VAL B 362 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.85e+00
  bond pdb=" N   VAL B 147 "
       pdb=" CA  VAL B 147 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.86e+00
  bond pdb=" N   PHE B 356 "
       pdb=" CA  PHE B 356 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.23e-02 6.61e+03 7.86e+00
  ... (remaining 22357 not shown)

  Histogram of bond angle deviations from ideal:
       99.74 -   106.59: 610
      106.59 -   113.44: 25083
      113.44 -   120.29: 7801
      120.29 -   127.14: 6598
      127.14 -   133.99: 121
  Bond angle restraints: 40213
  Sorted by residual:
  angle pdb=" N   ASP C  38 "
        pdb=" CA  ASP C  38 "
        pdb=" C   ASP C  38 "
      ideal   model   delta    sigma   weight residual
     108.00  116.00   -8.00 1.48e+00 4.57e-01 2.92e+01
  angle pdb=" N   ARG A 370 "
        pdb=" CA  ARG A 370 "
        pdb=" C   ARG A 370 "
      ideal   model   delta    sigma   weight residual
     113.97  107.57    6.40 1.28e+00 6.10e-01 2.50e+01
  angle pdb=" N   ARG D 173 "
        pdb=" CA  ARG D 173 "
        pdb=" C   ARG D 173 "
      ideal   model   delta    sigma   weight residual
     113.23  107.15    6.08 1.24e+00 6.50e-01 2.40e+01
  angle pdb=" N   ARG B  77 "
        pdb=" CA  ARG B  77 "
        pdb=" C   ARG B  77 "
      ideal   model   delta    sigma   weight residual
     112.86  106.91    5.95 1.22e+00 6.72e-01 2.38e+01
  angle pdb=" N   LYS B 361 "
        pdb=" CA  LYS B 361 "
        pdb=" C   LYS B 361 "
      ideal   model   delta    sigma   weight residual
     110.44  104.90    5.54 1.20e+00 6.94e-01 2.13e+01
  ... (remaining 40208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9741
       17.95 -    35.89: 592
       35.89 -    53.84: 213
       53.84 -    71.78: 62
       71.78 -    89.73: 15
  Dihedral angle restraints: 10623
    sinusoidal: 5712
      harmonic: 4911
  Sorted by residual:
  dihedral pdb=" CD  ARG A 346 "
           pdb=" NE  ARG A 346 "
           pdb=" CZ  ARG A 346 "
           pdb=" NH1 ARG A 346 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -56.24   56.24     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" CA  GLN A 446 "
           pdb=" C   GLN A 446 "
           pdb=" N   ASP A 447 "
           pdb=" CA  ASP A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  VAL E  26 "
           pdb=" C   VAL E  26 "
           pdb=" N   VAL E  27 "
           pdb=" CA  VAL E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.63  -19.37     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 10620 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1140
       0.035 -    0.070: 356
       0.070 -    0.105: 115
       0.105 -    0.141: 80
       0.141 -    0.176: 9
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CA  MET B  32 "
            pdb=" N   MET B  32 "
            pdb=" C   MET B  32 "
            pdb=" CB  MET B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CA  VAL B 147 "
            pdb=" N   VAL B 147 "
            pdb=" C   VAL B 147 "
            pdb=" CB  VAL B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  LEU B 192 "
            pdb=" N   LEU B 192 "
            pdb=" C   LEU B 192 "
            pdb=" CB  LEU B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1697 not shown)

  Planarity restraints: 3435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 346 "    0.948 9.50e-02 1.11e+02   3.17e-01 1.06e+02
        pdb=" NE  ARG A 346 "   -0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 346 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 346 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG A 346 "   -0.007 2.00e-02 2.50e+03
        pdb="HH12 ARG A 346 "    0.010 2.00e-02 2.50e+03
        pdb="HH21 ARG A 346 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 346 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  77 "   -0.338 9.50e-02 1.11e+02   1.13e-01 1.43e+01
        pdb=" NE  ARG B  77 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  77 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  77 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  77 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG B  77 "    0.016 2.00e-02 2.50e+03
        pdb="HH12 ARG B  77 "   -0.007 2.00e-02 2.50e+03
        pdb="HH21 ARG B  77 "    0.011 2.00e-02 2.50e+03
        pdb="HH22 ARG B  77 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 212 "   -0.338 9.50e-02 1.11e+02   1.13e-01 1.39e+01
        pdb=" NE  ARG A 212 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 212 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 212 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 212 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 212 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 212 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 212 "   -0.007 2.00e-02 2.50e+03
        pdb="HH22 ARG A 212 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 3432 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 311
        2.03 -     2.67: 31681
        2.67 -     3.32: 61427
        3.32 -     3.96: 78771
        3.96 -     4.60: 124421
  Nonbonded interactions: 296611
  Sorted by model distance:
  nonbonded pdb=" H   GLY B  55 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     1.391 1.850
  nonbonded pdb=" OD2 ASP B 300 "
            pdb="HD22 ASN B 302 "
     model   vdw
     1.469 1.850
  nonbonded pdb=" HG  SER B 112 "
            pdb=" OE2 GLU B 127 "
     model   vdw
     1.508 1.850
  nonbonded pdb=" O   TYR A 548 "
            pdb=" HG  SER A 551 "
     model   vdw
     1.539 1.850
  nonbonded pdb=" OD2 ASP B 303 "
            pdb=" H   LEU B 326 "
     model   vdw
     1.544 1.850
  ... (remaining 296606 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.00 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:             2.350
  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:             0.340
  Extract box with map and model:          10.800
  Check model and map are aligned:         0.310
  Set scattering table:                    0.200
  Process input model:                     71.510
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   88.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11516  Z= 0.233
  Angle     :  0.686   7.999  15654  Z= 0.434
  Chirality :  0.045   0.176   1700
  Planarity :  0.012   0.412   2062
  Dihedral  : 13.350  89.727   4165
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.72 (0.22), residues: 1428
  helix:  0.61 (0.30), residues: 304
  sheet: -0.57 (0.24), residues: 443
  loop : -0.82 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 745 
 HIS   0.002   0.001   HIS B 165 
 PHE   0.020   0.001   PHE A 347 
 TYR   0.018   0.001   TYR A 230 
 ARG   0.006   0.001   ARG B  77 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.5228
  time to fit residues: 113.9267
Evaluate side-chains
  116 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 110 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 753 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11516  Z= 0.235
  Angle     :  0.528   4.796  15654  Z= 0.287
  Chirality :  0.043   0.147   1700
  Planarity :  0.004   0.049   2062
  Dihedral  :  4.522  21.259   1580
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  5.47 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.48 (0.22), residues: 1428
  helix:  0.95 (0.30), residues: 306
  sheet: -0.35 (0.24), residues: 445
  loop : -0.81 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  93 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.003   0.000   ARG A 346 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 TYR cc_start: 0.8698 (m-80) cc_final: 0.8442 (m-80)
REVERT: A  582 ASP cc_start: 0.7213 (m-30) cc_final: 0.6946 (m-30)
REVERT: A  589 ASP cc_start: 0.8318 (t0) cc_final: 0.7724 (t70)
REVERT: E   64 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8505 (mtp)
  outliers start: 11
  outliers final: 9
  residues processed: 128
  average time/residue: 0.5211
  time to fit residues: 95.8272
Evaluate side-chains
  120 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 71 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 138 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 127 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11516  Z= 0.141
  Angle     :  0.465   4.793  15654  Z= 0.250
  Chirality :  0.042   0.151   1700
  Planarity :  0.003   0.033   2062
  Dihedral  :  4.135  19.387   1580
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.71 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.12 (0.22), residues: 1428
  helix:  1.35 (0.30), residues: 307
  sheet: -0.04 (0.24), residues: 450
  loop : -0.72 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.002   0.000   HIS A 280 
 PHE   0.010   0.001   PHE A 718 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.001   0.000   ARG B 281 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 1.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 TYR cc_start: 0.8701 (m-80) cc_final: 0.8424 (m-80)
REVERT: A  252 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7989 (mmtm)
REVERT: A  582 ASP cc_start: 0.7222 (m-30) cc_final: 0.7017 (m-30)
REVERT: A  589 ASP cc_start: 0.8277 (t0) cc_final: 0.7723 (t70)
REVERT: E   64 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8446 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 127
  average time/residue: 0.6104
  time to fit residues: 109.5978
Evaluate side-chains
  120 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0980
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0770
   chunk 128 optimal weight:    1.9990
   chunk 136 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11516  Z= 0.153
  Angle     :  0.455   4.699  15654  Z= 0.243
  Chirality :  0.042   0.148   1700
  Planarity :  0.003   0.033   2062
  Dihedral  :  3.963  18.959   1580
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  6.79 %
    Favored  : 91.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.07 (0.23), residues: 1428
  helix:  1.55 (0.31), residues: 307
  sheet:  0.14 (0.24), residues: 442
  loop : -0.68 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.002   0.000   HIS A 280 
 PHE   0.008   0.001   PHE A 718 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.002   0.000   ARG B 243 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  589 ASP cc_start: 0.8284 (t0) cc_final: 0.7849 (t70)
REVERT: E   64 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8438 (mtp)
  outliers start: 15
  outliers final: 11
  residues processed: 119
  average time/residue: 0.5466
  time to fit residues: 92.7830
Evaluate side-chains
  121 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 69 optimal weight:    0.6980
   chunk 122 optimal weight:    0.5980
   chunk 34 optimal weight:    0.1980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11516  Z= 0.177
  Angle     :  0.454   4.301  15654  Z= 0.243
  Chirality :  0.042   0.145   1700
  Planarity :  0.003   0.032   2062
  Dihedral  :  3.925  19.477   1580
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.37 %
    Favored  : 91.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.13 (0.23), residues: 1428
  helix:  1.64 (0.31), residues: 307
  sheet:  0.17 (0.25), residues: 441
  loop : -0.66 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 745 
 HIS   0.002   0.000   HIS A 280 
 PHE   0.010   0.001   PHE A 791 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.002   0.000   ARG B 243 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.4859 (tpt) cc_final: 0.4205 (tpt)
REVERT: E   64 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8473 (mtp)
  outliers start: 15
  outliers final: 11
  residues processed: 122
  average time/residue: 0.5800
  time to fit residues: 101.3419
Evaluate side-chains
  121 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 136 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   chunk 71 optimal weight:    2.9990
   chunk 131 optimal weight:    0.7980
   overall best weight:    1.3502

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11516  Z= 0.184
  Angle     :  0.455   4.202  15654  Z= 0.243
  Chirality :  0.042   0.145   1700
  Planarity :  0.003   0.031   2062
  Dihedral  :  3.886  19.662   1580
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.87 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.15 (0.23), residues: 1428
  helix:  1.70 (0.31), residues: 307
  sheet:  0.18 (0.25), residues: 439
  loop : -0.66 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 745 
 HIS   0.001   0.000   HIS A 280 
 PHE   0.010   0.001   PHE A 791 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.002   0.000   ARG B 243 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 2.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   64 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8441 (mtp)
  outliers start: 15
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5603
  time to fit residues: 97.1523
Evaluate side-chains
  121 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 76 optimal weight:    9.9990
   chunk 135 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 62 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11516  Z= 0.269
  Angle     :  0.488   4.676  15654  Z= 0.263
  Chirality :  0.043   0.142   1700
  Planarity :  0.003   0.036   2062
  Dihedral  :  4.059  20.802   1580
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.20 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.01 (0.23), residues: 1428
  helix:  1.56 (0.31), residues: 306
  sheet:  0.00 (0.24), residues: 442
  loop : -0.69 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 745 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.015   0.001   PHE A 791 
 TYR   0.014   0.001   TYR A 585 
 ARG   0.002   0.000   ARG A 346 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   64 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8491 (mtp)
  outliers start: 15
  outliers final: 13
  residues processed: 124
  average time/residue: 0.5721
  time to fit residues: 101.7813
Evaluate side-chains
  123 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   chunk 123 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11516  Z= 0.144
  Angle     :  0.445   4.199  15654  Z= 0.237
  Chirality :  0.042   0.146   1700
  Planarity :  0.003   0.030   2062
  Dihedral  :  3.843  20.054   1580
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.86 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.15 (0.23), residues: 1428
  helix:  1.77 (0.31), residues: 307
  sheet:  0.09 (0.24), residues: 439
  loop : -0.63 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.001   0.000   HIS A 280 
 PHE   0.009   0.001   PHE A 354 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.002   0.000   ARG B 243 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 1.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  215 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7655 (mmm160)
  outliers start: 12
  outliers final: 11
  residues processed: 121
  average time/residue: 0.5910
  time to fit residues: 102.0160
Evaluate side-chains
  119 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 2.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11516  Z= 0.235
  Angle     :  0.473   4.301  15654  Z= 0.253
  Chirality :  0.042   0.144   1700
  Planarity :  0.003   0.032   2062
  Dihedral  :  3.932  20.505   1580
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.20 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.05 (0.23), residues: 1428
  helix:  1.67 (0.31), residues: 306
  sheet:  0.00 (0.24), residues: 441
  loop : -0.64 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 745 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.013   0.001   PHE A 791 
 TYR   0.013   0.001   TYR D 184 
 ARG   0.002   0.000   ARG A 346 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 10
  residues processed: 118
  average time/residue: 0.5562
  time to fit residues: 94.1187
Evaluate side-chains
  120 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain D residue  117 MET
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 140 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0030
   chunk 86 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.5790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11516  Z= 0.118
  Angle     :  0.430   4.116  15654  Z= 0.227
  Chirality :  0.041   0.145   1700
  Planarity :  0.003   0.033   2062
  Dihedral  :  3.674  19.023   1580
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.20 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.30 (0.23), residues: 1428
  helix:  1.95 (0.31), residues: 307
  sheet:  0.14 (0.24), residues: 439
  loop : -0.53 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.002   0.000   HIS A 280 
 PHE   0.009   0.001   PHE A 354 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.001   0.000   ARG A 314 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 9
  residues processed: 124
  average time/residue: 0.5603
  time to fit residues: 98.7982
Evaluate side-chains
  120 residues out of total 1207 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 98 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.170515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.105537 restraints weight = 37610.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.112357 restraints weight = 18938.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.113979 restraints weight = 11861.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  11516  Z= 0.363
  Angle     :  0.534   4.592  15654  Z= 0.291
  Chirality :  0.044   0.145   1700
  Planarity :  0.004   0.050   2062
  Dihedral  :  4.200  21.650   1580
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.20 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.08 (0.22), residues: 1428
  helix:  1.47 (0.31), residues: 306
  sheet: -0.05 (0.24), residues: 432
  loop : -0.70 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 745 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.021   0.002   PHE A 791 
 TYR   0.018   0.002   TYR A 585 
 ARG   0.003   0.000   ARG B 295 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4181.57 seconds
wall clock time: 74 minutes 29.18 seconds (4469.18 seconds total)