Starting phenix.real_space_refine
on Fri Jun 20 01:19:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_14242.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_14242.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_14242.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_14242.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r1w_14242/06_2025/7r1w_14242.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.27, per 1000 atoms: 0.49
  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: 5.68
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 1.97
  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: 8.74

  Time building geometry restraints manager: 6.99 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:             3.240
  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:             0.370
  Extract box with map and model:          0.900
  Check model and map are aligned:         0.160
  Set scattering table:                    0.200
  Process input model:                     49.460
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.420
-------------------------------------------------------------------------------
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 : 8.79
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (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
 TRP   0.031   0.002   TRP G   1 
 HIS   0.069   0.003   HIS G   6 
 PHE   0.017   0.001   PHE E  74 
 TYR   0.021   0.001   TYR A 142 
 ARG   0.039   0.001   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12550 (  494)
  hydrogen bonds       : angle       6.29811 ( 1479)
  SS BOND              : bond        0.00352 (    1)
  SS BOND              : angle       1.77817 (    2)
  covalent geometry    : bond        0.00570 (12082)
  covalent geometry    : angle       0.68605 (16420)
  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  : 1.914 
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: 0.4946
  time to fit residues: 79.8899
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  : 2.045 
-------------------------------------------------------------------------------
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 124 optimal weight:    4.9990
   chunk 112 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.110823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.083107 restraints weight = 77966.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.086944 restraints weight = 26508.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.089340 restraints weight = 14353.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12084  Z= 0.122
  Angle     :  0.520   7.263  16422  Z= 0.281
  Chirality :  0.043   0.155   1785
  Planarity :  0.004   0.061   2163
  Dihedral  :  4.525  52.393   1657
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.09 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.89 %
    Favored  : 94.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.20), residues: 1493
  helix:  0.62 (0.29), residues: 329
  sheet: -1.19 (0.22), residues: 461
  loop : -2.42 (0.21), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.005   0.001   HIS G   6 
 PHE   0.009   0.001   PHE A 426 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.006   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  494)
  hydrogen bonds       : angle       4.79746 ( 1479)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.86504 (    2)
  covalent geometry    : bond        0.00271 (12082)
  covalent geometry    : angle       0.52031 (16420)
  Misc. bond           : bond        0.00340 (    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
  102 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 2.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.6922 (tmm) cc_final: 0.6647 (tmm)
REVERT: A  401 ASP cc_start: 0.7960 (t0) cc_final: 0.7672 (t0)
REVERT: C   81 ASP cc_start: 0.8257 (t0) cc_final: 0.7733 (t0)
REVERT: D   34 GLU cc_start: 0.9112 (mp0) cc_final: 0.8867 (mp0)
REVERT: E   46 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8503 (pp)
REVERT: E   47 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8238 (mmp-170)
REVERT: E   50 MET cc_start: 0.8003 (mtp) cc_final: 0.7713 (mtp)
  outliers start: 8
  outliers final: 5
  residues processed: 99
  average time/residue: 0.5961
  time to fit residues: 90.9683
Evaluate side-chains
  90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 1.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   46 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 39 optimal weight:    3.9990
   chunk 141 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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
B 368 GLN
D  82 ASN
D 102 HIS
E  52 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.104744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.076858 restraints weight = 78291.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.080478 restraints weight = 27178.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.082740 restraints weight = 14958.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  12084  Z= 0.184
  Angle     :  0.524   5.740  16422  Z= 0.284
  Chirality :  0.043   0.149   1785
  Planarity :  0.004   0.056   2163
  Dihedral  :  4.379  38.085   1657
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.62 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  5.68 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.21), residues: 1493
  helix:  0.90 (0.29), residues: 329
  sheet: -1.01 (0.22), residues: 475
  loop : -2.18 (0.21), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 776 
 HIS   0.007   0.002   HIS G   6 
 PHE   0.010   0.001   PHE E  74 
 TYR   0.016   0.001   TYR D 184 
 ARG   0.003   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  494)
  hydrogen bonds       : angle       4.65275 ( 1479)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       0.83662 (    2)
  covalent geometry    : bond        0.00405 (12082)
  covalent geometry    : angle       0.52363 (16420)
  Misc. bond           : bond        0.00322 (    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
  104 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 1.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.8011 (tmm) cc_final: 0.7564 (tmm)
REVERT: A  325 MET cc_start: 0.7071 (tmm) cc_final: 0.6771 (tmm)
REVERT: A  401 ASP cc_start: 0.8020 (t0) cc_final: 0.7752 (t0)
REVERT: C   81 ASP cc_start: 0.8316 (t0) cc_final: 0.7841 (t0)
REVERT: D  148 SER cc_start: 0.9046 (m) cc_final: 0.8802 (p)
REVERT: E   50 MET cc_start: 0.8268 (mtp) cc_final: 0.8038 (mtp)
REVERT: E   97 SER cc_start: 0.9255 (m) cc_final: 0.8988 (t)
  outliers start: 14
  outliers final: 12
  residues processed: 100
  average time/residue: 0.4653
  time to fit residues: 70.3187
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 1.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
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  248 ASP
Chi-restraints excluded: chain D residue   56 GLU
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  205 TYR
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 112 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.103493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.075682 restraints weight = 79522.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.079252 restraints weight = 27540.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081486 restraints weight = 15182.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088  12084  Z= 0.188
  Angle     :  0.504   4.438  16422  Z= 0.274
  Chirality :  0.043   0.147   1785
  Planarity :  0.004   0.043   2163
  Dihedral  :  4.283  36.189   1657
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.35 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.21), residues: 1493
  helix:  1.21 (0.29), residues: 325
  sheet: -0.82 (0.23), residues: 471
  loop : -2.02 (0.21), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.021   0.001   TYR A 142 
 ARG   0.005   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  494)
  hydrogen bonds       : angle       4.56409 ( 1479)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.72827 (    2)
  covalent geometry    : bond        0.00420 (12082)
  covalent geometry    : angle       0.50392 (16420)
  Misc. bond           : bond        0.00129 (    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
  96 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.906 
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  109 MET cc_start: 0.8008 (tmm) cc_final: 0.7647 (tmm)
REVERT: A  325 MET cc_start: 0.7171 (tmm) cc_final: 0.6885 (tmm)
REVERT: A  401 ASP cc_start: 0.7982 (t0) cc_final: 0.7739 (t0)
REVERT: C   81 ASP cc_start: 0.8344 (t0) cc_final: 0.7925 (t0)
REVERT: D  148 SER cc_start: 0.9095 (m) cc_final: 0.8882 (p)
REVERT: E   97 SER cc_start: 0.9254 (m) cc_final: 0.9022 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 93
  average time/residue: 0.4820
  time to fit residues: 67.2762
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 1.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  254 ILE
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   56 GLU
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  205 TYR
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 126 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 145 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
D 230 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 = 0.3735 r_free = 0.3735 target = 0.102046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.074077 restraints weight = 79603.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.077644 restraints weight = 27793.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.079865 restraints weight = 15383.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  12084  Z= 0.172
  Angle     :  0.494   4.641  16422  Z= 0.266
  Chirality :  0.042   0.144   1785
  Planarity :  0.004   0.043   2163
  Dihedral  :  4.226  32.967   1657
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.16 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.97 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.21), residues: 1493
  helix:  1.39 (0.29), residues: 322
  sheet: -0.67 (0.23), residues: 473
  loop : -1.87 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.010   0.001   PHE A 197 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.003   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03407 (  494)
  hydrogen bonds       : angle       4.48403 ( 1479)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       0.69398 (    2)
  covalent geometry    : bond        0.00387 (12082)
  covalent geometry    : angle       0.49389 (16420)
  Misc. bond           : bond        0.00150 (    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
  94 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 1.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7940 (tmm) cc_final: 0.7581 (tmm)
REVERT: A  325 MET cc_start: 0.7213 (tmm) cc_final: 0.6978 (tmm)
REVERT: A  401 ASP cc_start: 0.7971 (t0) cc_final: 0.7722 (t0)
REVERT: C   81 ASP cc_start: 0.8374 (t0) cc_final: 0.7948 (t0)
REVERT: E   97 SER cc_start: 0.9301 (m) cc_final: 0.9098 (t)
  outliers start: 13
  outliers final: 12
  residues processed: 91
  average time/residue: 0.4958
  time to fit residues: 66.9667
Evaluate side-chains
  85 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
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 A residue  741 MET
Chi-restraints excluded: chain B residue  248 ASP
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 145 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.101398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.073659 restraints weight = 79078.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.077162 restraints weight = 27526.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.079372 restraints weight = 15269.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  12084  Z= 0.162
  Angle     :  0.487   4.513  16422  Z= 0.262
  Chirality :  0.042   0.140   1785
  Planarity :  0.003   0.041   2163
  Dihedral  :  4.239  31.711   1657
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.62 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.60 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.21), residues: 1493
  helix:  1.57 (0.29), residues: 322
  sheet: -0.51 (0.23), residues: 465
  loop : -1.85 (0.21), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP G   1 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.009   0.001   PHE A 140 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.003   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  494)
  hydrogen bonds       : angle       4.41845 ( 1479)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.67985 (    2)
  covalent geometry    : bond        0.00364 (12082)
  covalent geometry    : angle       0.48695 (16420)
  Misc. bond           : bond        0.00176 (    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
  98 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 1.847 
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: A  109 MET cc_start: 0.7954 (tmm) cc_final: 0.7584 (tmm)
REVERT: A  325 MET cc_start: 0.7203 (tmm) cc_final: 0.6954 (tmm)
REVERT: A  401 ASP cc_start: 0.7987 (t0) cc_final: 0.7727 (t0)
REVERT: C   81 ASP cc_start: 0.8348 (t0) cc_final: 0.7068 (p0)
  outliers start: 15
  outliers final: 12
  residues processed: 94
  average time/residue: 0.5236
  time to fit residues: 72.2987
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 1.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
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  741 MET
Chi-restraints excluded: chain B residue  248 ASP
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   10 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 94 optimal weight:    0.2980
   chunk 134 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.100439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.073083 restraints weight = 80098.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.076478 restraints weight = 27600.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.078623 restraints weight = 15243.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  12084  Z= 0.196
  Angle     :  0.512   5.239  16422  Z= 0.276
  Chirality :  0.043   0.144   1785
  Planarity :  0.004   0.042   2163
  Dihedral  :  4.251  28.636   1657
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.69 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.23 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.21), residues: 1493
  helix:  1.59 (0.29), residues: 322
  sheet: -0.52 (0.23), residues: 462
  loop : -1.70 (0.22), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G   1 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.010   0.001   PHE A 140 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.003   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03476 (  494)
  hydrogen bonds       : angle       4.47727 ( 1479)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.71061 (    2)
  covalent geometry    : bond        0.00439 (12082)
  covalent geometry    : angle       0.51198 (16420)
  Misc. bond           : bond        0.00153 (    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
  97 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.990 
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  109 MET cc_start: 0.7898 (tmm) cc_final: 0.7521 (tmm)
REVERT: A  325 MET cc_start: 0.7276 (tmm) cc_final: 0.7043 (tmm)
REVERT: A  401 ASP cc_start: 0.8002 (t0) cc_final: 0.7748 (t0)
REVERT: C   81 ASP cc_start: 0.8368 (t0) cc_final: 0.7212 (p0)
REVERT: D   74 ASP cc_start: 0.8985 (t0) cc_final: 0.8752 (t70)
  outliers start: 19
  outliers final: 19
  residues processed: 92
  average time/residue: 0.5421
  time to fit residues: 73.5439
Evaluate side-chains
  92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 2.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 TYR
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  514 THR
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   75 LEU
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 E residue   28 TYR
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain G residue    2 ASN
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 15 optimal weight:    3.9990
   chunk 92 optimal weight:    0.4980
   chunk 56 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 143 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.101028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.073522 restraints weight = 79268.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.076986 restraints weight = 27385.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.079140 restraints weight = 15119.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  12084  Z= 0.127
  Angle     :  0.488   7.027  16422  Z= 0.260
  Chirality :  0.042   0.140   1785
  Planarity :  0.003   0.040   2163
  Dihedral  :  4.160  26.346   1657
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.09 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 10.10 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.21), residues: 1493
  helix:  1.80 (0.29), residues: 322
  sheet: -0.40 (0.23), residues: 459
  loop : -1.61 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.010   0.001   PHE A 140 
 TYR   0.019   0.001   TYR C  41 
 ARG   0.003   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (  494)
  hydrogen bonds       : angle       4.33457 ( 1479)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.63012 (    2)
  covalent geometry    : bond        0.00290 (12082)
  covalent geometry    : angle       0.48751 (16420)
  Misc. bond           : bond        0.00199 (    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: 15
    poor density    : 77
  time to evaluate  : 1.819 
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: A  109 MET cc_start: 0.7926 (tmm) cc_final: 0.7545 (tmm)
REVERT: A  325 MET cc_start: 0.7237 (tmm) cc_final: 0.7011 (tmm)
REVERT: A  401 ASP cc_start: 0.7990 (t0) cc_final: 0.7582 (t0)
REVERT: C   81 ASP cc_start: 0.8361 (t0) cc_final: 0.7221 (p0)
REVERT: D   74 ASP cc_start: 0.8977 (t0) cc_final: 0.8735 (t70)
  outliers start: 15
  outliers final: 14
  residues processed: 88
  average time/residue: 0.5000
  time to fit residues: 65.6179
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 1.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  459 ASN
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   75 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 563 ASN
B 336 ASN
D  70 GLN
G   2 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.098354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.070676 restraints weight = 80544.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.074046 restraints weight = 28387.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.076170 restraints weight = 15894.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.126  12084  Z= 0.297
  Angle     :  0.573   6.475  16422  Z= 0.312
  Chirality :  0.044   0.150   1785
  Planarity :  0.004   0.042   2163
  Dihedral  :  4.397  29.727   1657
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.83 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.18 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.21), residues: 1493
  helix:  1.48 (0.29), residues: 325
  sheet: -0.58 (0.23), residues: 470
  loop : -1.70 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 776 
 HIS   0.006   0.001   HIS B 165 
 PHE   0.014   0.002   PHE E  74 
 TYR   0.014   0.002   TYR D 184 
 ARG   0.004   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  494)
  hydrogen bonds       : angle       4.66622 ( 1479)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.92526 (    2)
  covalent geometry    : bond        0.00661 (12082)
  covalent geometry    : angle       0.57255 (16420)
  Misc. bond           : bond        0.00085 (    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
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 3.773 
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: A  109 MET cc_start: 0.7958 (tmm) cc_final: 0.7573 (tmm)
REVERT: A  325 MET cc_start: 0.7352 (tmm) cc_final: 0.7075 (tmm)
REVERT: C   81 ASP cc_start: 0.8416 (t0) cc_final: 0.7376 (p0)
REVERT: D   74 ASP cc_start: 0.9004 (t70) cc_final: 0.8774 (t70)
REVERT: D  183 GLU cc_start: 0.8661 (tp30) cc_final: 0.8428 (tp30)
  outliers start: 18
  outliers final: 17
  residues processed: 84
  average time/residue: 0.5468
  time to fit residues: 67.8065
Evaluate side-chains
  88 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 1.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  459 ASN
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  514 THR
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   75 LEU
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 E residue   28 TYR
Chi-restraints excluded: chain E residue   83 HIS
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 101 optimal weight:    0.0570
   chunk 46 optimal weight:    0.4980
   chunk 105 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0370
   chunk 70 optimal weight:    2.9990
   chunk 127 optimal weight:    0.5980
   chunk 104 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    0.3776

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.100979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.073477 restraints weight = 79371.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076930 restraints weight = 27216.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.079079 restraints weight = 14989.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12084  Z= 0.090
  Angle     :  0.489   6.886  16422  Z= 0.260
  Chirality :  0.043   0.141   1785
  Planarity :  0.003   0.042   2163
  Dihedral  :  4.179  25.456   1657
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.82 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.89 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.22), residues: 1493
  helix:  1.98 (0.29), residues: 322
  sheet: -0.33 (0.23), residues: 459
  loop : -1.53 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 348 
 HIS   0.007   0.001   HIS G   6 
 PHE   0.011   0.001   PHE A 140 
 TYR   0.016   0.001   TYR D 184 
 ARG   0.004   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  494)
  hydrogen bonds       : angle       4.28949 ( 1479)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.53542 (    2)
  covalent geometry    : bond        0.00203 (12082)
  covalent geometry    : angle       0.48867 (16420)
  Misc. bond           : bond        0.00250 (    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
  81 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 1.827 
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  109 MET cc_start: 0.7948 (tmm) cc_final: 0.7544 (tmm)
REVERT: A  325 MET cc_start: 0.7247 (tmm) cc_final: 0.7035 (tmm)
REVERT: C   81 ASP cc_start: 0.8365 (t0) cc_final: 0.7325 (p0)
REVERT: D   74 ASP cc_start: 0.8954 (t0) cc_final: 0.8710 (t70)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.5419
  time to fit residues: 62.9646
Evaluate side-chains
  81 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 1.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 TYR
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  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 96 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 128 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.099458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.071847 restraints weight = 80020.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.075244 restraints weight = 27951.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.077371 restraints weight = 15629.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  12084  Z= 0.195
  Angle     :  0.515   6.285  16422  Z= 0.277
  Chirality :  0.042   0.140   1785
  Planarity :  0.004   0.038   2163
  Dihedral  :  4.206  25.037   1657
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.89 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.89 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.22), residues: 1493
  helix:  1.90 (0.29), residues: 322
  sheet: -0.39 (0.23), residues: 462
  loop : -1.48 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 393 
 HIS   0.006   0.001   HIS G   6 
 PHE   0.011   0.001   PHE A 140 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.003   0.000   ARG G   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  494)
  hydrogen bonds       : angle       4.41136 ( 1479)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.66793 (    2)
  covalent geometry    : bond        0.00442 (12082)
  covalent geometry    : angle       0.51548 (16420)
  Misc. bond           : bond        0.00207 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7069.50 seconds
wall clock time: 122 minutes 30.44 seconds (7350.44 seconds total)