Starting phenix.real_space_refine
on Wed Mar  4 12:18:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_20764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_20764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_20764.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_20764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ugh_20764/03_2026/6ugh_20764.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          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: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1}
          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: 2.36, per 1000 atoms: 0.17
  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: 1.10
  Conformation dependent library (CDL) restraints added in 409.8 milliseconds
  

  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: 0.32
  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: 3.38

  Time building geometry restraints manager: 1.57 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:             4.740
  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:             0.080
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.570
-------------------------------------------------------------------------------
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 : 3.14
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (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
 ARG   0.017   0.001   ARG A 220 
 TYR   0.027   0.003   TYR A 560 
 PHE   0.037   0.003   PHE A 602 
 TRP   0.031   0.003   TRP A 612 
 HIS   0.007   0.002   HIS B 266 

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

*********************** 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  : 0.356 
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: 0.7703 (mt)
REVERT: A  499 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7106 (mt-10)
REVERT: A  627 ASN cc_start: 0.8948 (t0) cc_final: 0.8595 (t0)
REVERT: B   83 VAL cc_start: 0.8216 (t) cc_final: 0.7996 (t)
REVERT: B   99 ASP cc_start: 0.6068 (t0) cc_final: 0.5843 (t0)
REVERT: B  122 TYR cc_start: 0.6996 (m-80) cc_final: 0.6638 (m-80)
REVERT: B  123 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6229 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2234
  time to fit residues: 64.1432
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  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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
A 290 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.168724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.150970 restraints weight = 28367.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 1.88
r_work: 0.3730 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7152  Z= 0.152
  Angle     :  0.666   7.050   9747  Z= 0.359
  Chirality :  0.047   0.151   1087
  Planarity :  0.005   0.041   1262
  Dihedral  :  6.117  24.691    954
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.84 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.27), residues: 879
  helix: -1.55 (0.33), residues: 190
  sheet: -0.69 (0.30), residues: 271
  loop : -1.39 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  49 
 TYR   0.020   0.002   TYR A 283 
 PHE   0.020   0.002   PHE A 277 
 TRP   0.011   0.001   TRP A 603 
 HIS   0.006   0.001   HIS A 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7152)
  covalent geometry    : angle       0.66553 ( 9747)
  hydrogen bonds       : bond        0.04762 (  237)
  hydrogen bonds       : angle       6.32901 (  669)

*********************** 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
  208 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 195
  time to evaluate  : 0.349 
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: 0.8381 (mtm180) cc_final: 0.8089 (mtm180)
REVERT: A  219 ASP cc_start: 0.7641 (m-30) cc_final: 0.7384 (m-30)
REVERT: A  283 TYR cc_start: 0.7584 (t80) cc_final: 0.7342 (t80)
REVERT: A  432 ILE cc_start: 0.8516 (pt) cc_final: 0.8245 (mt)
REVERT: A  499 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: A  617 VAL cc_start: 0.8062 (t) cc_final: 0.7723 (p)
REVERT: B  122 TYR cc_start: 0.7229 (m-80) cc_final: 0.6481 (m-80)
REVERT: B  153 ASP cc_start: 0.7267 (t70) cc_final: 0.6357 (t0)
REVERT: B  298 ASP cc_start: 0.8417 (t0) cc_final: 0.8077 (t70)
  outliers start: 13
  outliers final: 10
  residues processed: 202
  average time/residue: 0.2085
  time to fit residues: 54.1032
Evaluate side-chains
  191 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 181
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 336 GLN
A 396 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.167287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.149725 restraints weight = 28408.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.74
r_work: 0.3690 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    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 = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3441

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= 0.297
  Angle     :  0.681   6.654   9747  Z= 0.372
  Chirality :  0.048   0.162   1087
  Planarity :  0.005   0.043   1262
  Dihedral  :  6.125  26.375    954
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.12 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 12.86 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.26), residues: 879
  helix: -1.35 (0.32), residues: 192
  sheet: -1.01 (0.29), residues: 268
  loop : -1.51 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  62 
 TYR   0.019   0.002   TYR A 342 
 PHE   0.028   0.002   PHE A 440 
 TRP   0.012   0.002   TRP A 404 
 HIS   0.005   0.002   HIS A 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 ( 7152)
  covalent geometry    : angle       0.68118 ( 9747)
  hydrogen bonds       : bond        0.04760 (  237)
  hydrogen bonds       : angle       6.32270 (  669)

*********************** 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: 24
    poor density    : 183
  time to evaluate  : 0.322 
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  166 ASP cc_start: 0.5729 (t0) cc_final: 0.4744 (t0)
REVERT: A  219 ASP cc_start: 0.7730 (m-30) cc_final: 0.7480 (m-30)
REVERT: A  260 LEU cc_start: 0.8522 (mt) cc_final: 0.8321 (mt)
REVERT: A  283 TYR cc_start: 0.7715 (t80) cc_final: 0.7485 (t80)
REVERT: A  436 LEU cc_start: 0.8257 (mt) cc_final: 0.8016 (mt)
REVERT: A  499 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7764 (mt-10)
REVERT: A  579 TRP cc_start: 0.7737 (m100) cc_final: 0.7050 (m100)
REVERT: A  602 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7807 (t80)
REVERT: A  617 VAL cc_start: 0.8230 (t) cc_final: 0.7947 (p)
REVERT: A  621 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6863 (t)
REVERT: B  122 TYR cc_start: 0.7529 (m-80) cc_final: 0.7295 (m-80)
  outliers start: 24
  outliers final: 14
  residues processed: 198
  average time/residue: 0.2228
  time to fit residues: 55.7136
Evaluate side-chains
  189 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  621 VAL
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 31 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 58 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 3 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  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.169720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.152222 restraints weight = 27981.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 1.74
r_work: 0.3739 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    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 = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3786

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= 0.129
  Angle     :  0.582   6.165   9747  Z= 0.311
  Chirality :  0.045   0.142   1087
  Planarity :  0.004   0.040   1262
  Dihedral  :  5.564  24.063    954
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.19 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.27), residues: 879
  helix: -0.66 (0.34), residues: 191
  sheet: -0.96 (0.30), residues: 262
  loop : -1.22 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  68 
 TYR   0.017   0.002   TYR A 342 
 PHE   0.019   0.002   PHE A 255 
 TRP   0.008   0.001   TRP B  54 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7152)
  covalent geometry    : angle       0.58166 ( 9747)
  hydrogen bonds       : bond        0.03661 (  237)
  hydrogen bonds       : angle       5.75961 (  669)

*********************** 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
  201 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.341 
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  113 PHE cc_start: 0.8441 (t80) cc_final: 0.8236 (t80)
REVERT: A  219 ASP cc_start: 0.7649 (m-30) cc_final: 0.7384 (m-30)
REVERT: A  260 LEU cc_start: 0.8441 (mt) cc_final: 0.8204 (mt)
REVERT: A  283 TYR cc_start: 0.7698 (t80) cc_final: 0.7413 (t80)
REVERT: A  499 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7698 (mt-10)
REVERT: A  579 TRP cc_start: 0.7706 (m100) cc_final: 0.7002 (m100)
REVERT: A  617 VAL cc_start: 0.8163 (t) cc_final: 0.7871 (p)
REVERT: A  621 VAL cc_start: 0.6909 (OUTLIER) cc_final: 0.6702 (t)
REVERT: B  122 TYR cc_start: 0.7441 (m-80) cc_final: 0.7107 (m-10)
REVERT: B  126 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6834 (m-30)
REVERT: B  160 LEU cc_start: 0.8839 (mm) cc_final: 0.8530 (pp)
  outliers start: 18
  outliers final: 11
  residues processed: 192
  average time/residue: 0.2213
  time to fit residues: 53.9336
Evaluate side-chains
  192 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 179
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  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  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
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  276 GLU
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 60 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.165139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.146714 restraints weight = 28550.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 1.88
r_work: 0.3668 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    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 = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7152  Z= 0.250
  Angle     :  0.623   6.038   9747  Z= 0.337
  Chirality :  0.046   0.148   1087
  Planarity :  0.005   0.044   1262
  Dihedral  :  5.685  23.080    954
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.69 %
    Favored  : 94.20 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.27), residues: 879
  helix: -0.60 (0.33), residues: 191
  sheet: -1.14 (0.30), residues: 262
  loop : -1.34 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  62 
 TYR   0.019   0.002   TYR A 342 
 PHE   0.022   0.002   PHE A 440 
 TRP   0.010   0.001   TRP A 404 
 HIS   0.004   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 7152)
  covalent geometry    : angle       0.62332 ( 9747)
  hydrogen bonds       : bond        0.03954 (  237)
  hydrogen bonds       : angle       5.93187 (  669)

*********************** 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
  204 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.274 
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  166 ASP cc_start: 0.5742 (t0) cc_final: 0.5388 (t0)
REVERT: A  219 ASP cc_start: 0.7810 (m-30) cc_final: 0.7500 (m-30)
REVERT: A  260 LEU cc_start: 0.8461 (mt) cc_final: 0.8228 (mt)
REVERT: A  283 TYR cc_start: 0.7745 (t80) cc_final: 0.7472 (t80)
REVERT: A  284 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8211 (tp)
REVERT: A  579 TRP cc_start: 0.7800 (m100) cc_final: 0.7025 (m100)
REVERT: A  617 VAL cc_start: 0.8236 (t) cc_final: 0.7934 (p)
REVERT: A  621 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6748 (t)
REVERT: B   70 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6729 (mt-10)
REVERT: B  126 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6923 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 192
  average time/residue: 0.2311
  time to fit residues: 55.6111
Evaluate side-chains
  195 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  375 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.169919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.152316 restraints weight = 27843.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.75
r_work: 0.3734 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    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 = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7152  Z= 0.114
  Angle     :  0.557   5.900   9747  Z= 0.297
  Chirality :  0.044   0.139   1087
  Planarity :  0.004   0.041   1262
  Dihedral  :  5.250  21.508    954
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.64 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.84 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.27), residues: 879
  helix:  0.03 (0.35), residues: 190
  sheet: -1.11 (0.30), residues: 258
  loop : -1.13 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 568 
 TYR   0.017   0.002   TYR A 342 
 PHE   0.015   0.001   PHE B 299 
 TRP   0.007   0.001   TRP B  54 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7152)
  covalent geometry    : angle       0.55724 ( 9747)
  hydrogen bonds       : bond        0.03284 (  237)
  hydrogen bonds       : angle       5.46904 (  669)

*********************** 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
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.344 
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: A   19 ASP cc_start: 0.8135 (t0) cc_final: 0.7813 (t0)
REVERT: A  219 ASP cc_start: 0.7634 (m-30) cc_final: 0.7363 (m-30)
REVERT: A  260 LEU cc_start: 0.8400 (mt) cc_final: 0.8149 (mt)
REVERT: A  283 TYR cc_start: 0.7695 (t80) cc_final: 0.7418 (t80)
REVERT: A  284 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (tp)
REVERT: A  499 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7480 (mt-10)
REVERT: A  617 VAL cc_start: 0.8157 (t) cc_final: 0.7871 (p)
REVERT: A  621 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6639 (t)
REVERT: B  107 GLU cc_start: 0.6799 (tp30) cc_final: 0.6560 (tp30)
REVERT: B  122 TYR cc_start: 0.7467 (m-80) cc_final: 0.7153 (m-80)
REVERT: B  126 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6924 (m-30)
REVERT: B  160 LEU cc_start: 0.8838 (mm) cc_final: 0.8507 (pp)
  outliers start: 16
  outliers final: 12
  residues processed: 195
  average time/residue: 0.2191
  time to fit residues: 54.1888
Evaluate side-chains
  196 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  284 LEU
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  450 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  602 PHE
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
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 20 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.151372 restraints weight = 28169.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.80
r_work: 0.3723 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3596 r_free = 0.3596    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 = 0.3596 r_free = 0.3596    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7152  Z= 0.126
  Angle     :  0.556   5.853   9747  Z= 0.293
  Chirality :  0.044   0.138   1087
  Planarity :  0.004   0.043   1262
  Dihedral  :  5.135  20.712    954
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.64 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.28), residues: 879
  helix:  0.45 (0.36), residues: 190
  sheet: -1.11 (0.30), residues: 260
  loop : -1.07 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 568 
 TYR   0.017   0.002   TYR A 342 
 PHE   0.017   0.001   PHE B 299 
 TRP   0.014   0.001   TRP A 404 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7152)
  covalent geometry    : angle       0.55638 ( 9747)
  hydrogen bonds       : bond        0.03123 (  237)
  hydrogen bonds       : angle       5.37564 (  669)

*********************** 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
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.350 
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  166 ASP cc_start: 0.5736 (t0) cc_final: 0.5263 (t0)
REVERT: A  219 ASP cc_start: 0.7632 (m-30) cc_final: 0.7399 (m-30)
REVERT: A  260 LEU cc_start: 0.8398 (mt) cc_final: 0.8142 (mt)
REVERT: A  283 TYR cc_start: 0.7752 (t80) cc_final: 0.7490 (t80)
REVERT: A  284 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8246 (tp)
REVERT: A  499 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7554 (mt-10)
REVERT: A  617 VAL cc_start: 0.8143 (t) cc_final: 0.7844 (p)
REVERT: A  621 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.6610 (t)
REVERT: B   28 GLU cc_start: 0.6527 (mp0) cc_final: 0.5920 (mp0)
REVERT: B  107 GLU cc_start: 0.6823 (tp30) cc_final: 0.6589 (tp30)
REVERT: B  122 TYR cc_start: 0.7464 (m-80) cc_final: 0.7144 (m-80)
REVERT: B  126 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6939 (m-30)
REVERT: B  156 GLN cc_start: 0.7773 (mp10) cc_final: 0.7544 (mp10)
REVERT: B  160 LEU cc_start: 0.8871 (mm) cc_final: 0.8528 (pp)
  outliers start: 16
  outliers final: 11
  residues processed: 195
  average time/residue: 0.2271
  time to fit residues: 56.5568
Evaluate side-chains
  194 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  284 LEU
Chi-restraints excluded: chain A residue  342 TYR
Chi-restraints excluded: chain A residue  345 LEU
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  621 VAL
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  283 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.163987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.145207 restraints weight = 28379.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 1.90
r_work: 0.3649 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    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 = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   7152  Z= 0.269
  Angle     :  0.630   5.769   9747  Z= 0.339
  Chirality :  0.046   0.146   1087
  Planarity :  0.006   0.056   1262
  Dihedral  :  5.465  19.807    954
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.60 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.45 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.27), residues: 879
  helix:  0.04 (0.34), residues: 191
  sheet: -1.32 (0.30), residues: 252
  loop : -1.30 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  62 
 TYR   0.020   0.002   TYR A 342 
 PHE   0.028   0.002   PHE B 299 
 TRP   0.011   0.001   TRP A 404 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 7152)
  covalent geometry    : angle       0.63043 ( 9747)
  hydrogen bonds       : bond        0.03728 (  237)
  hydrogen bonds       : angle       5.74287 (  669)

*********************** 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
  208 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 181
  time to evaluate  : 0.341 
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  109 GLN cc_start: 0.8354 (tt0) cc_final: 0.8140 (tt0)
REVERT: A  166 ASP cc_start: 0.6044 (t0) cc_final: 0.5255 (t0)
REVERT: A  194 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8467 (m)
REVERT: A  248 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6805 (mtmm)
REVERT: A  260 LEU cc_start: 0.8471 (mt) cc_final: 0.8236 (mt)
REVERT: A  283 TYR cc_start: 0.7881 (t80) cc_final: 0.7659 (t80)
REVERT: A  284 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: A  617 VAL cc_start: 0.8242 (t) cc_final: 0.7940 (p)
REVERT: A  621 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6751 (t)
REVERT: B  126 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6964 (m-30)
  outliers start: 27
  outliers final: 19
  residues processed: 195
  average time/residue: 0.2215
  time to fit residues: 54.4146
Evaluate side-chains
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  116 TYR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  248 LYS
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  440 PHE
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  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  146 ASP
Chi-restraints excluded: chain B residue  188 GLU
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 10 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.166796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.148570 restraints weight = 28442.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.85
r_work: 0.3693 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7152  Z= 0.120
  Angle     :  0.564   5.647   9747  Z= 0.300
  Chirality :  0.045   0.142   1087
  Planarity :  0.005   0.041   1262
  Dihedral  :  5.172  19.747    954
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.21 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.10 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.28), residues: 879
  helix:  0.40 (0.35), residues: 190
  sheet: -1.18 (0.31), residues: 250
  loop : -1.15 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  49 
 TYR   0.018   0.002   TYR A 342 
 PHE   0.027   0.002   PHE B 299 
 TRP   0.011   0.001   TRP A 404 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7152)
  covalent geometry    : angle       0.56404 ( 9747)
  hydrogen bonds       : bond        0.03234 (  237)
  hydrogen bonds       : angle       5.39625 (  669)

*********************** 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  : 0.390 
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   19 ASP cc_start: 0.8177 (t0) cc_final: 0.7826 (t0)
REVERT: A  166 ASP cc_start: 0.5880 (t0) cc_final: 0.5225 (t0)
REVERT: A  248 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6782 (mtmm)
REVERT: A  260 LEU cc_start: 0.8404 (mt) cc_final: 0.8145 (mt)
REVERT: A  617 VAL cc_start: 0.8132 (t) cc_final: 0.7851 (p)
REVERT: A  621 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6677 (t)
REVERT: B   28 GLU cc_start: 0.6570 (mp0) cc_final: 0.5991 (mp0)
REVERT: B  107 GLU cc_start: 0.6715 (tp30) cc_final: 0.6513 (tp30)
REVERT: B  126 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6983 (m-30)
REVERT: B  160 LEU cc_start: 0.8867 (mm) cc_final: 0.8497 (pp)
REVERT: B  162 SER cc_start: 0.8697 (t) cc_final: 0.8338 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 188
  average time/residue: 0.2234
  time to fit residues: 53.0044
Evaluate side-chains
  190 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  342 TYR
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  602 PHE
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
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 54 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0870
   chunk 71 optimal weight:    0.0000
   chunk 60 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.2168

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.166574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.147454 restraints weight = 28525.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.01
r_work: 0.3672 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3530 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    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 = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4881

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= 0.131
  Angle     :  0.559   5.723   9747  Z= 0.295
  Chirality :  0.044   0.139   1087
  Planarity :  0.005   0.041   1262
  Dihedral  :  5.045  19.566    954
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.23 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.28), residues: 879
  helix:  0.57 (0.35), residues: 190
  sheet: -1.17 (0.31), residues: 250
  loop : -1.13 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  62 
 TYR   0.017   0.002   TYR A 342 
 PHE   0.036   0.002   PHE A  50 
 TRP   0.021   0.001   TRP A 404 
 HIS   0.004   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7152)
  covalent geometry    : angle       0.55946 ( 9747)
  hydrogen bonds       : bond        0.03094 (  237)
  hydrogen bonds       : angle       5.28921 (  669)

********************** 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
  195 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.336 
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: 0.8211 (t0) cc_final: 0.7843 (t0)
REVERT: A  166 ASP cc_start: 0.5926 (t0) cc_final: 0.5424 (t0)
REVERT: A  248 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6715 (mtmm)
REVERT: A  617 VAL cc_start: 0.8123 (t) cc_final: 0.7829 (p)
REVERT: A  621 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6642 (t)
REVERT: B   28 GLU cc_start: 0.6584 (mp0) cc_final: 0.5988 (mp0)
REVERT: B  107 GLU cc_start: 0.6697 (tp30) cc_final: 0.6489 (tp30)
REVERT: B  126 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7061 (m-30)
  outliers start: 14
  outliers final: 9
  residues processed: 190
  average time/residue: 0.2360
  time to fit residues: 56.7849
Evaluate side-chains
  187 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  342 TYR
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  602 PHE
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  126 ASP
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 58 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   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 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.165509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.146292 restraints weight = 28704.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.00
r_work: 0.3657 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    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 = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4986

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= 0.186
  Angle     :  0.587   5.677   9747  Z= 0.313
  Chirality :  0.045   0.143   1087
  Planarity :  0.005   0.056   1262
  Dihedral  :  5.104  18.848    954
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.50 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.28), residues: 879
  helix:  0.53 (0.35), residues: 190
  sheet: -1.26 (0.31), residues: 250
  loop : -1.16 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  49 
 TYR   0.018   0.002   TYR A 342 
 PHE   0.039   0.002   PHE A  50 
 TRP   0.015   0.001   TRP A 404 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7152)
  covalent geometry    : angle       0.58698 ( 9747)
  hydrogen bonds       : bond        0.03328 (  237)
  hydrogen bonds       : angle       5.38717 (  669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3757.54 seconds
wall clock time: 64 minutes 22.42 seconds (3862.42 seconds total)