Starting phenix.real_space_refine
on Thu Jul 31 15:11:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ugh_20764/07_2025/6ugh_20764.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.001
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      35      5.16       5
     C    4438      2.51       5
     N    1200      2.21       5
     O    1301      1.98       5
     H    6716      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13690
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9309
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 594, 9309
          Classifications: {'peptide': 594}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 553}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "B"
      Number of atoms: 4381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 4381
          Classifications: {'peptide': 301}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 288}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 187 " occ=0.50
      ... (15 atoms not shown)
      pdb=" HE3AMET A 187 " occ=0.50
  Time building chain proxies: 7.82, per 1000 atoms: 0.57
  Number of scatterers: 13690
  At special positions: 0
  Unit cell: (85.8, 71.28, 137.28, 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      35     16.00
     O    1301      8.00
     N    1200      7.00
     C    4438      6.00
     H    6716      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.72
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 12 sheets defined
      26.1% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 58 through 62
      removed outlier: 3.527A  pdb=" N   ASN A  61 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.571A  pdb=" N   LEU A  73 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 81
    Processing helix  chain 'A' and resid 96 through 118
    Processing helix  chain 'A' and resid 131 through 143
      removed outlier: 3.535A  pdb=" N   ALA A 135 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG A 136 " --> pdb=" O   THR A 132 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   HIS A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 3.567A  pdb=" N   ARG A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 194
      removed outlier: 3.516A  pdb=" N  AMET A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 222
      removed outlier: 4.010A  pdb=" N   ARG A 220 " --> pdb=" O   HIS A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 236
      No H-bonds generated for 'chain 'A' and resid 234 through 236'
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 4.127A  pdb=" N   LEU A 253 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 4.307A  pdb=" N   GLU A 276 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   PHE A 277 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 291
      removed outlier: 3.899A  pdb=" N   LEU A 284 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLN A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 330 through 349
      removed outlier: 3.688A  pdb=" N   TYR A 337 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.750A  pdb=" N   LYS A 354 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 383
      removed outlier: 3.819A  pdb=" N   ALA A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 408
      removed outlier: 4.439A  pdb=" N   THR A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 411
      No H-bonds generated for 'chain 'A' and resid 409 through 411'
    Processing helix  chain 'A' and resid 442 through 444
      No H-bonds generated for 'chain 'A' and resid 442 through 444'
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 477 through 486
      removed outlier: 3.549A  pdb=" N   ASN A 482 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 499
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 3.585A  pdb=" N   HIS A 572 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 631
      removed outlier: 3.556A  pdb=" N   GLY A 630 " --> pdb=" O   ASN A 627 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG A 631 " --> pdb=" O   PRO A 628 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 627 through 631'
    Processing helix  chain 'B' and resid 69 through 73
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19
      removed outlier: 6.980A  pdb=" N   SER A  16 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   CYS A  42 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ARG A  18 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   LYS A  85 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 8.630A  pdb=" N   LEU A 123 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLY A  84 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE A 122 " --> pdb=" O   TRP A 152 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ARG A 154 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU A 124 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   PHE A 151 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ALA A 205 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   MET A 153 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLU A 207 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A 155 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   VAL A 204 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLY A  17 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 416
      removed outlier: 8.295A  pdb=" N   THR A 414 " --> pdb=" O   ILE A 386 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   VAL A 416 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL A 433 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   MET A 362 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ALA A 429 " --> pdb=" O   LYS A 458 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ASP A 460 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   ILE A 431 " --> pdb=" O   ASP A 460 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A 462 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL A 433 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ILE A 464 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 503
      removed outlier: 3.906A  pdb=" N   ILE A 586 " --> pdb=" O   HIS A 549 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   HIS A 549 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
      removed outlier: 11.747A  pdb=" N   GLN A 588 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
      removed outlier: 10.198A  pdb=" N   VAL A 547 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TYR A 468 " --> pdb=" O   THR A 520 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   THR A 520 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER A 470 " --> pdb=" O   CYS A 518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511
      removed outlier: 7.212A  pdb=" N   ILE A 563 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 541
      removed outlier: 6.466A  pdb=" N   CYS A 599 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 36
      removed outlier: 3.525A  pdb=" N   GLN B  30 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLY B  45 " --> pdb=" O   GLU B  32 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ALA B  34 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU B  43 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 89
      removed outlier: 3.528A  pdb=" N   GLY B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA B 102 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL B 103 " --> pdb=" O   CYS B 120 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   CYS B 120 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU B 105 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 133
      removed outlier: 3.673A  pdb=" N   THR B 130 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE B 149 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER B 162 " --> pdb=" O   ILE B 149 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL B 151 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 175
      removed outlier: 3.683A  pdb=" N   CYS B 172 " --> pdb=" O   CYS B 186 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B 192 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 220
      removed outlier: 6.550A  pdb=" N   GLY B 231 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   LEU B 218 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B 229 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   TRP B 220 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   VAL B 227 " --> pdb=" O   TRP B 220 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU B 249 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 263
      removed outlier: 3.781A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 300 through 305
      removed outlier: 7.057A  pdb=" N   VAL B 316 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA B 303 " --> pdb=" O   THR B 314 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR B 314 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TRP B 305 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   LEU B 312 " --> pdb=" O   TRP B 305 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    669 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.49

  Time building geometry restraints manager: 4.32 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6692
        1.03 -     1.23: 84
        1.23 -     1.42: 3007
        1.42 -     1.62: 4039
        1.62 -     1.81: 46
  Bond restraints: 13868
  Sorted by residual:
  bond pdb=" CG  PRO A 465 "
       pdb=" CD  PRO A 465 "
    ideal  model  delta    sigma   weight residual
    1.512  1.453  0.059 2.70e-02 1.37e+03 4.74e+00
  bond pdb=" CB  TRP A 189 "
       pdb=" CG  TRP A 189 "
    ideal  model  delta    sigma   weight residual
    1.498  1.434  0.064 3.10e-02 1.04e+03 4.26e+00
  bond pdb=" CB  PRO A 465 "
       pdb=" CG  PRO A 465 "
    ideal  model  delta    sigma   weight residual
    1.506  1.426  0.080 3.90e-02 6.57e+02 4.24e+00
  bond pdb=" CA  ASN A 627 "
       pdb=" C   ASN A 627 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.013 6.50e-03 2.37e+04 4.02e+00
  bond pdb=" CB  PRO A 501 "
       pdb=" CG  PRO A 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.392  0.100 5.00e-02 4.00e+02 4.02e+00
  ... (remaining 13863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 21259
        1.51 -     3.02: 3101
        3.02 -     4.52: 518
        4.52 -     6.03: 110
        6.03 -     7.54: 26
  Bond angle restraints: 25014
  Sorted by residual:
  angle pdb=" N   VAL B 248 "
        pdb=" CA  VAL B 248 "
        pdb=" C   VAL B 248 "
      ideal   model   delta    sigma   weight residual
     106.21  110.49   -4.28 1.07e+00 8.73e-01 1.60e+01
  angle pdb=" C   GLU A 276 "
        pdb=" N   PHE A 277 "
        pdb=" CA  PHE A 277 "
      ideal   model   delta    sigma   weight residual
     121.54  128.70   -7.16 1.91e+00 2.74e-01 1.40e+01
  angle pdb=" N   TYR A 560 "
        pdb=" CA  TYR A 560 "
        pdb=" C   TYR A 560 "
      ideal   model   delta    sigma   weight residual
     108.38  103.38    5.00 1.35e+00 5.49e-01 1.37e+01
  angle pdb=" N   GLY A 369 "
        pdb=" CA  GLY A 369 "
        pdb=" C   GLY A 369 "
      ideal   model   delta    sigma   weight residual
     112.34  119.38   -7.04 2.04e+00 2.40e-01 1.19e+01
  angle pdb=" N   VAL A 504 "
        pdb=" CA  VAL A 504 "
        pdb=" C   VAL A 504 "
      ideal   model   delta    sigma   weight residual
     108.06  112.47   -4.41 1.28e+00 6.10e-01 1.19e+01
  ... (remaining 25009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 5940
       16.70 -    33.40: 459
       33.40 -    50.09: 161
       50.09 -    66.79: 38
       66.79 -    83.49: 7
  Dihedral angle restraints: 6605
    sinusoidal: 3495
      harmonic: 3110
  Sorted by residual:
  dihedral pdb=" CA  ASP B 146 "
           pdb=" C   ASP B 146 "
           pdb=" N   ILE B 147 "
           pdb=" CA  ILE B 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.55  -33.45     0      5.00e+00 4.00e-02 4.48e+01
  dihedral pdb=" CA  SER A 434 "
           pdb=" C   SER A 434 "
           pdb=" N   GLU A 435 "
           pdb=" CA  GLU A 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.18   30.82     0      5.00e+00 4.00e-02 3.80e+01
  dihedral pdb=" CA  ILE A 530 "
           pdb=" C   ILE A 530 "
           pdb=" N   ASP A 531 "
           pdb=" CA  ASP A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.75  -28.25     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 6602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 657
       0.043 -    0.086: 299
       0.086 -    0.128: 114
       0.128 -    0.171: 14
       0.171 -    0.214: 3
  Chirality restraints: 1087
  Sorted by residual:
  chirality pdb=" CB  VAL A 155 "
            pdb=" CA  VAL A 155 "
            pdb=" CG1 VAL A 155 "
            pdb=" CG2 VAL A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CB  THR A 194 "
            pdb=" CA  THR A 194 "
            pdb=" OG1 THR A 194 "
            pdb=" CG2 THR A 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  ASP A 562 "
            pdb=" N   ASP A 562 "
            pdb=" C   ASP A 562 "
            pdb=" CB  ASP A 562 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.70e-01
  ... (remaining 1084 not shown)

  Planarity restraints: 2097
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 602 "   -0.013 2.00e-02 2.50e+03   2.88e-02 2.48e+01
        pdb=" CG  PHE A 602 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 602 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 602 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 602 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 602 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 602 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 602 "    0.062 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 602 "    0.031 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 602 "   -0.037 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 602 "   -0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 602 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 509 "   -0.008 2.00e-02 2.50e+03   1.84e-02 1.01e+01
        pdb=" CG  PHE A 509 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 509 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 509 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 509 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 509 "    0.003 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 509 "    0.037 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 509 "    0.024 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 509 "   -0.021 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 509 "   -0.006 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 509 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 560 "    0.001 2.00e-02 2.50e+03   1.49e-02 6.65e+00
        pdb=" CG  TYR A 560 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 560 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 560 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 560 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 560 "    0.002 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 560 "    0.032 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 560 "    0.011 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 560 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 560 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2094 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.87: 85
        1.87 -     2.55: 12944
        2.55 -     3.23: 41723
        3.23 -     3.92: 54010
        3.92 -     4.60: 87578
  Nonbonded interactions: 196340
  Sorted by model distance:
  nonbonded pdb=" HG  SER B 144 "
            pdb=" OD1 ASP B 146 "
     model   vdw
     1.186 2.450
  nonbonded pdb=" OE1 GLU B  28 "
            pdb=" HG  SER B  57 "
     model   vdw
     1.362 2.450
  nonbonded pdb=" HG  SER B 185 "
            pdb=" HE1 TRP B 195 "
     model   vdw
     1.383 2.100
  nonbonded pdb=" HG  SER B 142 "
            pdb=" HE1 TRP B 152 "
     model   vdw
     1.455 2.100
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" HH  TYR A 613 "
     model   vdw
     1.532 2.450
  ... (remaining 196335 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.020
  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:             0.230
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.170
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
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      :  0.009   0.100   7152  Z= 0.388
  Angle     :  0.901   7.540   9747  Z= 0.492
  Chirality :  0.054   0.214   1087
  Planarity :  0.005   0.063   1262
  Dihedral  : 13.449  83.492   2548
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  3.30 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.50 (0.26), residues: 879
  helix: -3.31 (0.25), residues: 177
  sheet: -0.55 (0.31), residues: 279
  loop : -1.60 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 612 
 HIS   0.007   0.002   HIS B 266 
 PHE   0.037   0.003   PHE A 602 
 TYR   0.027   0.003   TYR A 560 
 ARG   0.017   0.001   ARG A 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27881 (  237)
  hydrogen bonds       : angle       9.99173 (  669)
  covalent geometry    : bond        0.00938 ( 7152)
  covalent geometry    : angle       0.90137 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  227 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 LEU cc_start: 0.8271 (mt) cc_final: 0.7702 (mt)
REVERT: A  499 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7107 (mt-10)
REVERT: A  627 ASN cc_start: 0.8948 (t0) cc_final: 0.8595 (t0)
REVERT: B   99 ASP cc_start: 0.6068 (t0) cc_final: 0.5805 (t0)
REVERT: B  122 TYR cc_start: 0.6996 (m-80) cc_final: 0.6642 (m-80)
REVERT: B  123 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6228 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 227
  average time/residue: 0.5178
  time to fit residues: 148.5020
Evaluate side-chains
  176 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
A 191 ASN
A 251 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.170288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.152091 restraints weight = 28191.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.92
r_work: 0.3736 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3603 r_free = 0.3603    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7152  Z= 0.151
  Angle     :  0.656   7.054   9747  Z= 0.353
  Chirality :  0.047   0.146   1087
  Planarity :  0.005   0.043   1262
  Dihedral  :  6.083  25.136    954
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.07 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.21 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.87 (0.27), residues: 879
  helix: -1.68 (0.32), residues: 187
  sheet: -0.64 (0.30), residues: 271
  loop : -1.35 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 603 
 HIS   0.005   0.001   HIS A 272 
 PHE   0.018   0.002   PHE A 277 
 TYR   0.019   0.002   TYR A 283 
 ARG   0.006   0.000   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05597 (  237)
  hydrogen bonds       : angle       6.37819 (  669)
  covalent geometry    : bond        0.00331 ( 7152)
  covalent geometry    : angle       0.65608 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  203 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 192
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7936 (mtm180)
REVERT: A  219 ASP cc_start: 0.7671 (m-30) cc_final: 0.7430 (m-30)
REVERT: A  283 TYR cc_start: 0.7566 (t80) cc_final: 0.7318 (t80)
REVERT: A  499 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7554 (mt-10)
REVERT: A  617 VAL cc_start: 0.8067 (t) cc_final: 0.7734 (p)
REVERT: B  122 TYR cc_start: 0.7171 (m-80) cc_final: 0.6433 (m-80)
REVERT: B  123 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6613 (mm-30)
REVERT: B  153 ASP cc_start: 0.7205 (t70) cc_final: 0.6171 (t0)
REVERT: B  298 ASP cc_start: 0.8422 (t0) cc_final: 0.8124 (t70)
  outliers start: 11
  outliers final: 8
  residues processed: 198
  average time/residue: 0.4816
  time to fit residues: 122.5436
Evaluate side-chains
  188 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0980
   chunk 75 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    3.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A 289 GLN
A 290 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.165274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.146461 restraints weight = 28458.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.89
r_work: 0.3663 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
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      :  0.007   0.062   7152  Z= 0.301
  Angle     :  0.689   6.740   9747  Z= 0.375
  Chirality :  0.048   0.161   1087
  Planarity :  0.006   0.059   1262
  Dihedral  :  6.136  26.813    954
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.35 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.86 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -2.06 (0.26), residues: 879
  helix: -1.33 (0.32), residues: 192
  sheet: -1.03 (0.29), residues: 268
  loop : -1.50 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 404 
 HIS   0.006   0.002   HIS A 272 
 PHE   0.029   0.002   PHE A 440 
 TYR   0.019   0.002   TYR A 342 
 ARG   0.003   0.001   ARG B 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04855 (  237)
  hydrogen bonds       : angle       6.33496 (  669)
  covalent geometry    : bond        0.00666 ( 7152)
  covalent geometry    : angle       0.68863 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  207 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.5862 (t0) cc_final: 0.5120 (t0)
REVERT: A  219 ASP cc_start: 0.7856 (m-30) cc_final: 0.7546 (m-30)
REVERT: A  283 TYR cc_start: 0.7746 (t80) cc_final: 0.7513 (t80)
REVERT: A  470 SER cc_start: 0.9388 (m) cc_final: 0.9170 (p)
REVERT: A  499 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: A  579 TRP cc_start: 0.7828 (m100) cc_final: 0.7184 (m100)
REVERT: A  602 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7938 (t80)
REVERT: A  617 VAL cc_start: 0.8232 (t) cc_final: 0.7910 (p)
  outliers start: 22
  outliers final: 14
  residues processed: 199
  average time/residue: 0.5292
  time to fit residues: 133.9350
Evaluate side-chains
  186 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  300 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 412 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.170165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.152670 restraints weight = 27779.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 1.73
r_work: 0.3743 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3611 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7152  Z= 0.121
  Angle     :  0.578   6.177   9747  Z= 0.308
  Chirality :  0.045   0.143   1087
  Planarity :  0.005   0.039   1262
  Dihedral  :  5.520  23.748    954
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.30 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.99 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.27), residues: 879
  helix: -0.53 (0.34), residues: 191
  sheet: -0.98 (0.30), residues: 262
  loop : -1.21 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  54 
 HIS   0.004   0.001   HIS B 124 
 PHE   0.018   0.002   PHE B 299 
 TYR   0.016   0.002   TYR A 342 
 ARG   0.005   0.000   ARG B 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03607 (  237)
  hydrogen bonds       : angle       5.75151 (  669)
  covalent geometry    : bond        0.00269 ( 7152)
  covalent geometry    : angle       0.57814 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8082 (t0) cc_final: 0.7524 (t0)
REVERT: A  113 PHE cc_start: 0.8430 (t80) cc_final: 0.8228 (t80)
REVERT: A  219 ASP cc_start: 0.7628 (m-30) cc_final: 0.7355 (m-30)
REVERT: A  283 TYR cc_start: 0.7699 (t80) cc_final: 0.7442 (t80)
REVERT: A  499 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: A  579 TRP cc_start: 0.7806 (m100) cc_final: 0.7061 (m100)
REVERT: A  617 VAL cc_start: 0.8170 (t) cc_final: 0.7888 (p)
REVERT: B  107 GLU cc_start: 0.6795 (tp30) cc_final: 0.6583 (tp30)
REVERT: B  122 TYR cc_start: 0.7410 (m-80) cc_final: 0.7153 (m-80)
REVERT: B  126 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6860 (m-30)
REVERT: B  160 LEU cc_start: 0.8807 (mm) cc_final: 0.8524 (pp)
REVERT: B  276 GLU cc_start: 0.7672 (pt0) cc_final: 0.7448 (pt0)
  outliers start: 14
  outliers final: 10
  residues processed: 189
  average time/residue: 0.5371
  time to fit residues: 130.3449
Evaluate side-chains
  185 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0980
   chunk 16 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.170681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.153016 restraints weight = 27839.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 1.75
r_work: 0.3755 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7152  Z= 0.122
  Angle     :  0.556   5.937   9747  Z= 0.296
  Chirality :  0.045   0.140   1087
  Planarity :  0.004   0.041   1262
  Dihedral  :  5.287  23.380    954
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.10 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.85 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.29 (0.28), residues: 879
  helix: -0.03 (0.35), residues: 191
  sheet: -0.93 (0.31), residues: 262
  loop : -1.09 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 404 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.017   0.001   PHE A  50 
 TYR   0.017   0.002   TYR A 342 
 ARG   0.008   0.001   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  237)
  hydrogen bonds       : angle       5.57504 (  669)
  covalent geometry    : bond        0.00274 ( 7152)
  covalent geometry    : angle       0.55637 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.7664 (m-30) cc_final: 0.7361 (m-30)
REVERT: A  283 TYR cc_start: 0.7722 (t80) cc_final: 0.7472 (t80)
REVERT: A  284 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8156 (tp)
REVERT: A  499 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: A  617 VAL cc_start: 0.8163 (t) cc_final: 0.7855 (p)
REVERT: B  107 GLU cc_start: 0.6787 (tp30) cc_final: 0.6562 (tp30)
REVERT: B  122 TYR cc_start: 0.7396 (m-80) cc_final: 0.7009 (m-10)
REVERT: B  126 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6893 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 194
  average time/residue: 0.5023
  time to fit residues: 124.1414
Evaluate side-chains
  195 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A  79 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.168403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.150518 restraints weight = 28293.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.78
r_work: 0.3719 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7152  Z= 0.187
  Angle     :  0.580   6.090   9747  Z= 0.310
  Chirality :  0.045   0.141   1087
  Planarity :  0.005   0.040   1262
  Dihedral  :  5.306  22.282    954
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.01 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.25 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.34 (0.28), residues: 879
  helix:  0.03 (0.35), residues: 191
  sheet: -1.06 (0.30), residues: 259
  loop : -1.12 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 404 
 HIS   0.004   0.001   HIS A 190 
 PHE   0.024   0.002   PHE A  50 
 TYR   0.018   0.002   TYR A 342 
 ARG   0.011   0.001   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03436 (  237)
  hydrogen bonds       : angle       5.61340 (  669)
  covalent geometry    : bond        0.00416 ( 7152)
  covalent geometry    : angle       0.58003 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  206 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLN cc_start: 0.8220 (tt0) cc_final: 0.7973 (tt0)
REVERT: A  283 TYR cc_start: 0.7741 (t80) cc_final: 0.7497 (t80)
REVERT: A  284 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8190 (tp)
REVERT: A  499 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: A  617 VAL cc_start: 0.8211 (t) cc_final: 0.7908 (p)
REVERT: B  126 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6972 (m-30)
REVERT: B  160 LEU cc_start: 0.8851 (mm) cc_final: 0.8448 (pp)
  outliers start: 22
  outliers final: 18
  residues processed: 194
  average time/residue: 0.5178
  time to fit residues: 129.7715
Evaluate side-chains
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.169397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.151304 restraints weight = 28183.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.80
r_work: 0.3727 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7152  Z= 0.123
  Angle     :  0.543   5.867   9747  Z= 0.287
  Chirality :  0.044   0.140   1087
  Planarity :  0.004   0.042   1262
  Dihedral  :  5.083  21.107    954
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.21 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.18 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.20 (0.28), residues: 879
  helix:  0.41 (0.36), residues: 191
  sheet: -1.09 (0.30), residues: 264
  loop : -1.07 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 404 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.021   0.001   PHE A  50 
 TYR   0.017   0.002   TYR A 342 
 ARG   0.004   0.000   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  237)
  hydrogen bonds       : angle       5.38175 (  669)
  covalent geometry    : bond        0.00276 ( 7152)
  covalent geometry    : angle       0.54317 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  205 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 187
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8084 (t0) cc_final: 0.7720 (t0)
REVERT: A  109 GLN cc_start: 0.8166 (tt0) cc_final: 0.7912 (tt0)
REVERT: A  283 TYR cc_start: 0.7750 (t80) cc_final: 0.7512 (t80)
REVERT: A  284 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8240 (tp)
REVERT: A  499 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7494 (mt-10)
REVERT: A  617 VAL cc_start: 0.8129 (t) cc_final: 0.7825 (p)
REVERT: B  107 GLU cc_start: 0.6763 (tp30) cc_final: 0.6542 (tp30)
REVERT: B  126 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6984 (m-30)
REVERT: B  160 LEU cc_start: 0.8866 (mm) cc_final: 0.8453 (pp)
REVERT: B  276 GLU cc_start: 0.7876 (pt0) cc_final: 0.7650 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 197
  average time/residue: 0.4891
  time to fit residues: 123.2995
Evaluate side-chains
  196 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 4 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.153181 restraints weight = 27936.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.80
r_work: 0.3739 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7152  Z= 0.107
  Angle     :  0.537   5.876   9747  Z= 0.282
  Chirality :  0.044   0.139   1087
  Planarity :  0.004   0.044   1262
  Dihedral  :  4.904  19.614    954
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.87 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.24 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -0.99 (0.28), residues: 879
  helix:  0.85 (0.37), residues: 191
  sheet: -1.07 (0.30), residues: 264
  loop : -1.00 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 579 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.026   0.001   PHE A  50 
 TYR   0.017   0.002   TYR A 116 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02968 (  237)
  hydrogen bonds       : angle       5.18828 (  669)
  covalent geometry    : bond        0.00244 ( 7152)
  covalent geometry    : angle       0.53690 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 185
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  499 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: A  617 VAL cc_start: 0.8104 (t) cc_final: 0.7820 (p)
REVERT: B   28 GLU cc_start: 0.6409 (mp0) cc_final: 0.5804 (mp0)
REVERT: B  126 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6944 (m-30)
REVERT: B  160 LEU cc_start: 0.8838 (mm) cc_final: 0.8433 (pp)
REVERT: B  276 GLU cc_start: 0.7810 (pt0) cc_final: 0.7581 (pt0)
  outliers start: 15
  outliers final: 12
  residues processed: 193
  average time/residue: 0.5024
  time to fit residues: 123.7421
Evaluate side-chains
  193 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 180
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 75 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.1984

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.169640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.151546 restraints weight = 27933.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 1.80
r_work: 0.3733 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7152  Z= 0.127
  Angle     :  0.541   5.846   9747  Z= 0.285
  Chirality :  0.044   0.139   1087
  Planarity :  0.004   0.042   1262
  Dihedral  :  4.858  18.952    954
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.11 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -0.98 (0.28), residues: 879
  helix:  0.83 (0.37), residues: 191
  sheet: -1.03 (0.30), residues: 262
  loop : -1.01 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 579 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.019   0.001   PHE A  50 
 TYR   0.017   0.002   TYR A 342 
 ARG   0.004   0.000   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03023 (  237)
  hydrogen bonds       : angle       5.18187 (  669)
  covalent geometry    : bond        0.00287 ( 7152)
  covalent geometry    : angle       0.54074 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  195 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7906 (mtm180)
REVERT: A  166 ASP cc_start: 0.5717 (t0) cc_final: 0.5346 (t0)
REVERT: A  617 VAL cc_start: 0.8100 (t) cc_final: 0.7821 (p)
REVERT: B   28 GLU cc_start: 0.6476 (mp0) cc_final: 0.6171 (mp0)
REVERT: B  126 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6960 (m-30)
REVERT: B  160 LEU cc_start: 0.8864 (mm) cc_final: 0.8413 (pp)
REVERT: B  276 GLU cc_start: 0.7905 (pt0) cc_final: 0.7691 (pt0)
  outliers start: 15
  outliers final: 12
  residues processed: 188
  average time/residue: 0.5030
  time to fit residues: 120.3046
Evaluate side-chains
  190 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 64 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.167288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.149001 restraints weight = 28377.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.82
r_work: 0.3704 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7152  Z= 0.189
  Angle     :  0.570   5.767   9747  Z= 0.303
  Chirality :  0.045   0.144   1087
  Planarity :  0.005   0.043   1262
  Dihedral  :  5.035  18.370    954
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.24 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.11 (0.28), residues: 879
  helix:  0.67 (0.36), residues: 190
  sheet: -1.11 (0.30), residues: 255
  loop : -1.06 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 579 
 HIS   0.004   0.001   HIS A 190 
 PHE   0.020   0.002   PHE A  50 
 TYR   0.018   0.002   TYR A 342 
 ARG   0.005   0.001   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  237)
  hydrogen bonds       : angle       5.34586 (  669)
  covalent geometry    : bond        0.00423 ( 7152)
  covalent geometry    : angle       0.57024 ( 9747)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  148 is missing expected H atoms. Skipping.
Residue LYS  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue LYS  275 is missing expected H atoms. Skipping.
Residue LEU  299 is missing expected H atoms. Skipping.
Residue LYS  302 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  529 is missing expected H atoms. Skipping.
Residue ILE  530 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue SER  225 is missing expected H atoms. Skipping.
Residue LYS  243 is missing expected H atoms. Skipping.
Residue SER  244 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Evaluate side-chains
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8130 (t0) cc_final: 0.7743 (t0)
REVERT: A  166 ASP cc_start: 0.5915 (t0) cc_final: 0.5284 (t0)
REVERT: A  248 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6715 (mtmm)
REVERT: A  617 VAL cc_start: 0.8188 (t) cc_final: 0.7895 (p)
REVERT: B  126 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7016 (m-30)
REVERT: B  160 LEU cc_start: 0.8815 (mm) cc_final: 0.8386 (pp)
REVERT: B  276 GLU cc_start: 0.7970 (pt0) cc_final: 0.7744 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 192
  average time/residue: 0.5092
  time to fit residues: 124.1644
Evaluate side-chains
  193 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0570
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.7502

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.164903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.146516 restraints weight = 28900.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.91
r_work: 0.3682 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7152  Z= 0.157
  Angle     :  0.560   5.684   9747  Z= 0.296
  Chirality :  0.045   0.140   1087
  Planarity :  0.005   0.045   1262
  Dihedral  :  4.989  18.352    954
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.90 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    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: -1.06 (0.28), residues: 879
  helix:  0.75 (0.36), residues: 190
  sheet: -1.12 (0.31), residues: 254
  loop : -1.03 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 579 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.034   0.002   PHE A  50 
 TYR   0.018   0.002   TYR A 342 
 ARG   0.005   0.000   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03147 (  237)
  hydrogen bonds       : angle       5.29768 (  669)
  covalent geometry    : bond        0.00355 ( 7152)
  covalent geometry    : angle       0.56013 ( 9747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8014.10 seconds
wall clock time: 136 minutes 26.07 seconds (8186.07 seconds total)