Starting phenix.real_space_refine
on Thu Mar  5 14:36:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r1w_14242/03_2026/7r1w_14242.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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    7447      2.51       5
     N    2022      2.21       5
     O    2322      1.98       5
     H   11363      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23186
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 786, 12122
          Classifications: {'peptide': 786}
          Link IDs: {'PTRANS': 29, 'TRANS': 756}
    Chain: "B"
      Number of atoms: 5416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5416
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 11, 'TRANS': 350}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 844
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3346
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1291
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 167
          Classifications: {'peptide': 10}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 9}
  Time building chain proxies: 3.60, per 1000 atoms: 0.16
  Number of scatterers: 23186
  At special positions: 0
  Unit cell: (101.68, 134.48, 125.46, 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    2322      8.00
     N    2022      7.00
     C    7447      6.00
     H   11363      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.95
  Conformation dependent library (CDL) restraints added in 848.1 milliseconds
  

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2762

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 17 sheets defined
      23.2% alpha, 30.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
      removed outlier: 3.676A  pdb=" N   ILE A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 286'
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.727A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.714A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.660A  pdb=" N   LEU A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 500
      removed outlier: 3.952A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 500'
    Processing helix  chain 'A' and resid 542 through 550
      removed outlier: 4.361A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 553
      No H-bonds generated for 'chain 'A' and resid 551 through 553'
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.573A  pdb=" N   GLY A 695 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 733
      removed outlier: 3.617A  pdb=" N   VAL A 733 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 33
    Processing helix  chain 'C' and resid 34 through 39
      removed outlier: 3.997A  pdb=" N   ASP C  38 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 34 through 39'
    Processing helix  chain 'D' and resid 31 through 44
      removed outlier: 3.541A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN D  44 " --> pdb=" O   GLN D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.215A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 160 through 189
      removed outlier: 3.785A  pdb=" N   PHE D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 205
      removed outlier: 3.987A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 213
      removed outlier: 3.964A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 225
    Processing helix  chain 'D' and resid 227 through 240
      removed outlier: 3.955A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.773A  pdb=" N   HIS A  30 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A  86 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 7.501A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.638A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 3.859A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.767A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.912A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 12.237A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.827A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.531A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   GLN A 411 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ASP A 413 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 433
      removed outlier: 3.766A  pdb=" N   GLN A 466 " --> pdb=" O   ASN A 463 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 426 through 433
      removed outlier: 3.766A  pdb=" N   GLN A 466 " --> pdb=" O   ASN A 463 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 662 through 663
      removed outlier: 3.973A  pdb=" N   GLY A 662 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50
      removed outlier: 3.673A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 75
      removed outlier: 3.996A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 117
      removed outlier: 6.307A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.784A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.870A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.505A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.949A  pdb=" N   VAL B 305 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   THR B 318 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ALA B 307 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    531 hydrogen bonds defined for protein.
    1479 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: 5.97

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 11312
        1.03 -     1.23: 66
        1.23 -     1.42: 5227
        1.42 -     1.62: 6778
        1.62 -     1.82: 62
  Bond restraints: 23445
  Sorted by residual:
  bond pdb=" CA  ASN G   2 "
       pdb=" C   ASN G   2 "
    ideal  model  delta    sigma   weight residual
    1.533  1.398  0.135 9.60e-03 1.09e+04 1.99e+02
  bond pdb=" C   SER G   3 "
       pdb=" O   SER G   3 "
    ideal  model  delta    sigma   weight residual
    1.235  1.372 -0.137 1.26e-02 6.30e+03 1.18e+02
  bond pdb=" CA  HIS G   6 "
       pdb=" C   HIS G   6 "
    ideal  model  delta    sigma   weight residual
    1.523  1.388  0.135 1.34e-02 5.57e+03 1.02e+02
  bond pdb=" CA  SER G   7 "
       pdb=" C   SER G   7 "
    ideal  model  delta    sigma   weight residual
    1.525  1.398  0.127 1.29e-02 6.01e+03 9.75e+01
  bond pdb=" CA  SER G   3 "
       pdb=" C   SER G   3 "
    ideal  model  delta    sigma   weight residual
    1.523  1.401  0.122 1.34e-02 5.57e+03 8.27e+01
  ... (remaining 23440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.62: 42048
        3.62 -     7.24: 85
        7.24 -    10.86: 11
       10.86 -    14.48: 2
       14.48 -    18.10: 1
  Bond angle restraints: 42147
  Sorted by residual:
  angle pdb=" N   TYR G   8 "
        pdb=" CA  TYR G   8 "
        pdb=" C   TYR G   8 "
      ideal   model   delta    sigma   weight residual
     109.71  123.48  -13.77 1.41e+00 5.03e-01 9.53e+01
  angle pdb=" N   SER G   7 "
        pdb=" CA  SER G   7 "
        pdb=" C   SER G   7 "
      ideal   model   delta    sigma   weight residual
     107.75   89.65   18.10 1.86e+00 2.89e-01 9.46e+01
  angle pdb=" CA  SER G   7 "
        pdb=" C   SER G   7 "
        pdb=" N   TYR G   8 "
      ideal   model   delta    sigma   weight residual
     116.21  127.68  -11.47 1.36e+00 5.41e-01 7.11e+01
  angle pdb=" CA  HIS G   6 "
        pdb=" CB  HIS G   6 "
        pdb=" CG  HIS G   6 "
      ideal   model   delta    sigma   weight residual
     113.80  121.14   -7.34 1.00e+00 1.00e+00 5.38e+01
  angle pdb=" O   SER G   7 "
        pdb=" C   SER G   7 "
        pdb=" N   TYR G   8 "
      ideal   model   delta    sigma   weight residual
     122.87  113.93    8.94 1.23e+00 6.61e-01 5.28e+01
  ... (remaining 42142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 10043
       17.55 -    35.10: 794
       35.10 -    52.66: 224
       52.66 -    70.21: 49
       70.21 -    87.76: 13
  Dihedral angle restraints: 11123
    sinusoidal: 5982
      harmonic: 5141
  Sorted by residual:
  dihedral pdb=" CA  LEU A 699 "
           pdb=" C   LEU A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.56  -22.44     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  GLU C  39 "
           pdb=" C   GLU C  39 "
           pdb=" N   ALA C  40 "
           pdb=" CA  ALA C  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.68  -20.32     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C   SER G   7 "
           pdb=" N   SER G   7 "
           pdb=" CA  SER G   7 "
           pdb=" CB  SER G   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.64   -8.96     0      2.50e+00 1.60e-01 1.28e+01
  ... (remaining 11120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1590
       0.070 -    0.140: 181
       0.140 -    0.210: 9
       0.210 -    0.280: 3
       0.280 -    0.350: 2
  Chirality restraints: 1785
  Sorted by residual:
  chirality pdb=" CA  TRP G   1 "
            pdb=" N   TRP G   1 "
            pdb=" C   TRP G   1 "
            pdb=" CB  TRP G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.22    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  VAL G   5 "
            pdb=" N   VAL G   5 "
            pdb=" C   VAL G   5 "
            pdb=" CB  VAL G   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.73   -0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  ASN G   4 "
            pdb=" N   ASN G   4 "
            pdb=" C   ASN G   4 "
            pdb=" CB  ASN G   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1782 not shown)

  Planarity restraints: 3595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 427 "    0.113 2.00e-02 2.50e+03   1.19e-01 2.13e+02
        pdb=" CG  ASN A 427 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 427 "   -0.107 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 427 "   -0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN A 427 "    0.177 2.00e-02 2.50e+03
        pdb="HD22 ASN A 427 "   -0.172 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G   6 "    0.063 2.00e-02 2.50e+03   5.31e-02 5.63e+01
        pdb=" CG  HIS G   6 "   -0.112 2.00e-02 2.50e+03
        pdb=" ND1 HIS G   6 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 HIS G   6 "    0.050 2.00e-02 2.50e+03
        pdb=" CE1 HIS G   6 "    0.035 2.00e-02 2.50e+03
        pdb=" NE2 HIS G   6 "   -0.032 2.00e-02 2.50e+03
        pdb=" HD2 HIS G   6 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 HIS G   6 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 186 "   -0.020 2.00e-02 2.50e+03   2.99e-02 1.34e+01
        pdb=" CG  ASN B 186 "    0.064 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 186 "   -0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 186 "   -0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN B 186 "   -0.008 2.00e-02 2.50e+03
        pdb="HD22 ASN B 186 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 3592 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 262
        2.03 -     2.67: 33707
        2.67 -     3.31: 62877
        3.31 -     3.96: 82604
        3.96 -     4.60: 130185
  Nonbonded interactions: 309635
  Sorted by model distance:
  nonbonded pdb=" CH2 TRP G   1 "
            pdb=" CB  ASN G   4 "
     model   vdw
     1.387 3.450
  nonbonded pdb=" HG  SER A 502 "
            pdb=" OE1 GLN A 542 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HH  TYR A 674 "
            pdb=" OD2 ASP A 704 "
     model   vdw
     1.557 2.450
  nonbonded pdb=" H   LYS A 103 "
            pdb=" OE2 GLU A 171 "
     model   vdw
     1.561 2.450
  nonbonded pdb="HE21 GLN B 319 "
            pdb=" O   GLY B 354 "
     model   vdw
     1.583 2.450
  ... (remaining 309630 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:             4.590
  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:             0.130
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     22.520
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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      :  0.006   0.138  12084  Z= 0.361
  Angle     :  0.686  18.096  16422  Z= 0.415
  Chirality :  0.046   0.350   1785
  Planarity :  0.004   0.059   2163
  Dihedral  : 13.744  87.759   4374
  Min Nonbonded Distance : 1.387

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.69 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.24 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.20), residues: 1493
  helix:  0.02 (0.29), residues: 312
  sheet: -1.60 (0.21), residues: 460
  loop : -2.70 (0.20), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.039   0.001   ARG D  97 
 TYR   0.021   0.001   TYR A 142 
 PHE   0.017   0.001   PHE E  74 
 TRP   0.031   0.002   TRP G   1 
 HIS   0.069   0.003   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (12082)
  covalent geometry    : angle       0.68605 (16420)
  SS BOND              : bond        0.00352 (    1)
  SS BOND              : angle       1.77817 (    2)
  hydrogen bonds       : bond        0.12550 (  494)
  hydrogen bonds       : angle       6.29811 ( 1479)
  Misc. bond           : bond        0.05203 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.6859 (tmm) cc_final: 0.6575 (tmm)
REVERT: C   81 ASP cc_start: 0.8173 (t0) cc_final: 0.7678 (t0)
REVERT: D   34 GLU cc_start: 0.8988 (mp0) cc_final: 0.8717 (mp0)
REVERT: E   50 MET cc_start: 0.8133 (mtp) cc_final: 0.7927 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 109
  average time/residue: 0.2324
  time to fit residues: 37.2620
Evaluate side-chains
  80 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 561 GLN
B 168 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.106223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.078012 restraints weight = 79071.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.081682 restraints weight = 27752.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.084016 restraints weight = 15342.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.085379 restraints weight = 10910.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.086067 restraints weight = 8996.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.119  12084  Z= 0.227
  Angle     :  0.564   7.388  16422  Z= 0.308
  Chirality :  0.044   0.151   1785
  Planarity :  0.004   0.059   2163
  Dihedral  :  4.647  53.845   1657
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.49 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  5.52 %
    Favored  : 93.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.20), residues: 1493
  helix:  0.49 (0.29), residues: 329
  sheet: -1.28 (0.22), residues: 468
  loop : -2.46 (0.20), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  97 
 TYR   0.016   0.001   TYR D 184 
 PHE   0.012   0.001   PHE D  95 
 TRP   0.012   0.001   TRP A 776 
 HIS   0.009   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (12082)
  covalent geometry    : angle       0.56419 (16420)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.97692 (    2)
  hydrogen bonds       : bond        0.04157 (  494)
  hydrogen bonds       : angle       4.97611 ( 1479)
  Misc. bond           : bond        0.00572 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.7013 (tmm) cc_final: 0.6701 (tmm)
REVERT: C   81 ASP cc_start: 0.8265 (t0) cc_final: 0.7806 (t0)
REVERT: D  148 SER cc_start: 0.8955 (m) cc_final: 0.8726 (p)
REVERT: E   50 MET cc_start: 0.8190 (mtp) cc_final: 0.7945 (mtp)
REVERT: E   97 SER cc_start: 0.9172 (m) cc_final: 0.8885 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 95
  average time/residue: 0.2067
  time to fit residues: 29.6717
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain D residue   64 PHE
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 123 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 132 optimal weight:    0.6980
   chunk 146 optimal weight:    0.0050
   chunk 48 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
B 168 ASN
B 368 GLN
D  82 ASN
E  52 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.106287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.078254 restraints weight = 78458.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.081934 restraints weight = 27097.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.084245 restraints weight = 14846.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085522 restraints weight = 10522.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086316 restraints weight = 8731.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12084  Z= 0.120
  Angle     :  0.481   6.573  16422  Z= 0.259
  Chirality :  0.042   0.146   1785
  Planarity :  0.004   0.057   2163
  Dihedral  :  4.299  39.335   1657
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.75 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.55 %
    Favored  : 92.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.21), residues: 1493
  helix:  1.05 (0.29), residues: 329
  sheet: -0.96 (0.22), residues: 466
  loop : -2.21 (0.21), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G   9 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.004   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (12082)
  covalent geometry    : angle       0.48092 (16420)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.66577 (    2)
  hydrogen bonds       : bond        0.03516 (  494)
  hydrogen bonds       : angle       4.55266 ( 1479)
  Misc. bond           : bond        0.00225 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.7114 (tmm) cc_final: 0.6849 (tmm)
REVERT: A  394 PHE cc_start: 0.8611 (m-10) cc_final: 0.8308 (m-10)
REVERT: A  401 ASP cc_start: 0.8004 (t0) cc_final: 0.7733 (t0)
REVERT: C   81 ASP cc_start: 0.8277 (t0) cc_final: 0.7816 (t0)
REVERT: D  148 SER cc_start: 0.8952 (m) cc_final: 0.8735 (p)
REVERT: E   97 SER cc_start: 0.9184 (m) cc_final: 0.8922 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.2136
  time to fit residues: 30.8288
Evaluate side-chains
  84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 129 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
G   2 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.104353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.076431 restraints weight = 79245.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.080034 restraints weight = 27581.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.082280 restraints weight = 15209.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.083598 restraints weight = 10833.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.084230 restraints weight = 8942.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  12084  Z= 0.152
  Angle     :  0.484   4.696  16422  Z= 0.262
  Chirality :  0.042   0.146   1785
  Planarity :  0.004   0.050   2163
  Dihedral  :  4.192  34.097   1657
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.35 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.18 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.21), residues: 1493
  helix:  1.12 (0.29), residues: 331
  sheet: -0.80 (0.23), residues: 469
  loop : -2.01 (0.21), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   9 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.008   0.001   PHE E  74 
 TRP   0.010   0.001   TRP B 348 
 HIS   0.007   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12082)
  covalent geometry    : angle       0.48445 (16420)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.64453 (    2)
  hydrogen bonds       : bond        0.03347 (  494)
  hydrogen bonds       : angle       4.46199 ( 1479)
  Misc. bond           : bond        0.00191 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.7135 (tmm) cc_final: 0.6895 (tmm)
REVERT: A  394 PHE cc_start: 0.8659 (m-10) cc_final: 0.8303 (m-10)
REVERT: A  401 ASP cc_start: 0.7931 (t0) cc_final: 0.7712 (t0)
REVERT: C   81 ASP cc_start: 0.8304 (t0) cc_final: 0.7859 (t0)
REVERT: E   97 SER cc_start: 0.9229 (m) cc_final: 0.9000 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 95
  average time/residue: 0.2188
  time to fit residues: 31.0235
Evaluate side-chains
  91 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   79 GLN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0980
   chunk 100 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   chunk 5 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 146 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
G   2 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.104568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.076652 restraints weight = 78661.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.080225 restraints weight = 27189.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.082480 restraints weight = 14952.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.083814 restraints weight = 10646.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.084472 restraints weight = 8791.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12084  Z= 0.108
  Angle     :  0.457   5.226  16422  Z= 0.245
  Chirality :  0.042   0.143   1785
  Planarity :  0.003   0.042   2163
  Dihedral  :  4.043  28.029   1657
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.55 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.81 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.21), residues: 1493
  helix:  1.47 (0.29), residues: 328
  sheet: -0.62 (0.23), residues: 467
  loop : -1.81 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G   9 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.005   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (12082)
  covalent geometry    : angle       0.45655 (16420)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.52855 (    2)
  hydrogen bonds       : bond        0.03092 (  494)
  hydrogen bonds       : angle       4.27017 ( 1479)
  Misc. bond           : bond        0.00207 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7940 (t0) cc_final: 0.7685 (t0)
REVERT: C   81 ASP cc_start: 0.8308 (t0) cc_final: 0.7841 (t0)
REVERT: E   97 SER cc_start: 0.9217 (m) cc_final: 0.8998 (t)
  outliers start: 10
  outliers final: 10
  residues processed: 92
  average time/residue: 0.2126
  time to fit residues: 29.0311
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain G residue    2 ASN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 68 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 146 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0570
   overall best weight:    1.5304

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

Flipped N/Q/H residues before XYZ refinement:
G   2 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.103429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.075497 restraints weight = 79550.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.079070 restraints weight = 27575.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.081305 restraints weight = 15219.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.082624 restraints weight = 10856.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.083203 restraints weight = 8972.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  12084  Z= 0.149
  Angle     :  0.470   4.759  16422  Z= 0.252
  Chirality :  0.042   0.141   1785
  Planarity :  0.003   0.041   2163
  Dihedral  :  4.096  33.137   1657
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.29 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.05 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.21), residues: 1493
  helix:  1.52 (0.29), residues: 327
  sheet: -0.58 (0.23), residues: 464
  loop : -1.74 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G   9 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.007   0.001   PHE E  74 
 TRP   0.017   0.001   TRP G   1 
 HIS   0.006   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12082)
  covalent geometry    : angle       0.46970 (16420)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.61514 (    2)
  hydrogen bonds       : bond        0.03160 (  494)
  hydrogen bonds       : angle       4.29651 ( 1479)
  Misc. bond           : bond        0.00190 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7933 (t0) cc_final: 0.7681 (t0)
REVERT: C   81 ASP cc_start: 0.8340 (t0) cc_final: 0.7873 (t0)
REVERT: E   97 SER cc_start: 0.9247 (m) cc_final: 0.9039 (t)
  outliers start: 12
  outliers final: 11
  residues processed: 88
  average time/residue: 0.2131
  time to fit residues: 28.0174
Evaluate side-chains
  88 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain G residue    2 ASN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 134 optimal weight:    0.9980
   chunk 3 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
D 158 GLN
G   2 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.102348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.074489 restraints weight = 79513.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.078040 restraints weight = 27609.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.080217 restraints weight = 15254.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081538 restraints weight = 10924.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082276 restraints weight = 9029.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  12084  Z= 0.167
  Angle     :  0.482   5.242  16422  Z= 0.259
  Chirality :  0.042   0.139   1785
  Planarity :  0.003   0.041   2163
  Dihedral  :  4.161  42.082   1657
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.29 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.45 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.21), residues: 1493
  helix:  1.68 (0.29), residues: 321
  sheet: -0.57 (0.23), residues: 464
  loop : -1.65 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  33 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.008   0.001   PHE E  74 
 TRP   0.012   0.001   TRP B 393 
 HIS   0.006   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12082)
  covalent geometry    : angle       0.48170 (16420)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.64027 (    2)
  hydrogen bonds       : bond        0.03221 (  494)
  hydrogen bonds       : angle       4.31810 ( 1479)
  Misc. bond           : bond        0.00176 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7970 (t0) cc_final: 0.7720 (t0)
REVERT: C   81 ASP cc_start: 0.8351 (t0) cc_final: 0.7907 (t0)
REVERT: E   97 SER cc_start: 0.9255 (m) cc_final: 0.9052 (t)
  outliers start: 12
  outliers final: 11
  residues processed: 88
  average time/residue: 0.2279
  time to fit residues: 29.6968
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
D 102 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.101928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.074029 restraints weight = 79447.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.077510 restraints weight = 27578.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.079690 restraints weight = 15347.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.080981 restraints weight = 11021.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081594 restraints weight = 9140.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12084  Z= 0.164
  Angle     :  0.487   6.083  16422  Z= 0.261
  Chirality :  0.042   0.140   1785
  Planarity :  0.003   0.040   2163
  Dihedral  :  4.072  22.169   1657
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.76 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.21), residues: 1493
  helix:  1.77 (0.29), residues: 321
  sheet: -0.41 (0.23), residues: 460
  loop : -1.65 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  33 
 TYR   0.013   0.001   TYR D 184 
 PHE   0.008   0.001   PHE E  74 
 TRP   0.023   0.001   TRP G   1 
 HIS   0.005   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (12082)
  covalent geometry    : angle       0.48735 (16420)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       0.63822 (    2)
  hydrogen bonds       : bond        0.03224 (  494)
  hydrogen bonds       : angle       4.32088 ( 1479)
  Misc. bond           : bond        0.00189 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7960 (t0) cc_final: 0.7708 (t0)
REVERT: C   81 ASP cc_start: 0.8351 (t0) cc_final: 0.7139 (p0)
  outliers start: 12
  outliers final: 12
  residues processed: 89
  average time/residue: 0.2113
  time to fit residues: 27.9780
Evaluate side-chains
  90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain G residue    2 ASN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 143 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.100397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.072779 restraints weight = 79688.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.076233 restraints weight = 27953.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.078385 restraints weight = 15565.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.079634 restraints weight = 11161.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.080247 restraints weight = 9276.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  12084  Z= 0.193
  Angle     :  0.511   6.372  16422  Z= 0.276
  Chirality :  0.043   0.142   1785
  Planarity :  0.004   0.040   2163
  Dihedral  :  4.180  20.895   1657
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.23 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.21), residues: 1493
  helix:  1.75 (0.29), residues: 321
  sheet: -0.49 (0.23), residues: 464
  loop : -1.55 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  29 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.009   0.001   PHE E  74 
 TRP   0.011   0.001   TRP A 776 
 HIS   0.006   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (12082)
  covalent geometry    : angle       0.51068 (16420)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       0.64807 (    2)
  hydrogen bonds       : bond        0.03435 (  494)
  hydrogen bonds       : angle       4.43297 ( 1479)
  Misc. bond           : bond        0.00170 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7974 (t0) cc_final: 0.7726 (t0)
REVERT: C   81 ASP cc_start: 0.8351 (t0) cc_final: 0.7258 (p0)
  outliers start: 13
  outliers final: 12
  residues processed: 88
  average time/residue: 0.2466
  time to fit residues: 31.5620
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain G residue    2 ASN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 95 optimal weight:    4.9990
   chunk 137 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 143 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.101979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.074292 restraints weight = 79488.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.077804 restraints weight = 27591.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.079979 restraints weight = 15289.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081284 restraints weight = 10968.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.081842 restraints weight = 9083.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12084  Z= 0.104
  Angle     :  0.478   9.218  16422  Z= 0.252
  Chirality :  0.042   0.140   1785
  Planarity :  0.003   0.039   2163
  Dihedral  :  4.016  18.606   1657
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.02 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.22), residues: 1493
  helix:  2.00 (0.29), residues: 322
  sheet: -0.32 (0.23), residues: 459
  loop : -1.46 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   9 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.006   0.001   PHE E  74 
 TRP   0.014   0.001   TRP B 348 
 HIS   0.006   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12082)
  covalent geometry    : angle       0.47798 (16420)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.49644 (    2)
  hydrogen bonds       : bond        0.03033 (  494)
  hydrogen bonds       : angle       4.22316 ( 1479)
  Misc. bond           : bond        0.00248 (    1)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASP cc_start: 0.7925 (t0) cc_final: 0.7506 (t0)
REVERT: C   81 ASP cc_start: 0.8347 (t0) cc_final: 0.7284 (p0)
  outliers start: 11
  outliers final: 11
  residues processed: 84
  average time/residue: 0.2080
  time to fit residues: 26.2192
Evaluate side-chains
  84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain G residue    2 ASN
Chi-restraints excluded: chain G residue   10 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 125 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 119 optimal weight:    0.0770
   chunk 129 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.101306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073735 restraints weight = 79460.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.077197 restraints weight = 27743.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.079363 restraints weight = 15434.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.080639 restraints weight = 11071.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.081360 restraints weight = 9195.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  12084  Z= 0.143
  Angle     :  0.479   5.672  16422  Z= 0.256
  Chirality :  0.042   0.187   1785
  Planarity :  0.003   0.038   2163
  Dihedral  :  3.995  17.147   1657
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.02 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.22), residues: 1493
  helix:  2.02 (0.29), residues: 321
  sheet: -0.36 (0.23), residues: 459
  loop : -1.38 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   9 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.008   0.001   PHE E  74 
 TRP   0.012   0.001   TRP B 393 
 HIS   0.005   0.001   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12082)
  covalent geometry    : angle       0.47895 (16420)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.51591 (    2)
  hydrogen bonds       : bond        0.03142 (  494)
  hydrogen bonds       : angle       4.26532 ( 1479)
  Misc. bond           : bond        0.00217 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3623.46 seconds
wall clock time: 62 minutes 22.84 seconds (3742.84 seconds total)