Starting phenix.real_space_refine
on Fri Oct 23 03:16:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pb3_71452/10_2026/9pb3_71452.map"
  }
  resolution = 4.0
  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=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    5124      2.51       5
     N    1346      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8029
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 599
          Classifications: {'peptide': 71}
          Link IDs: {'TRANS': 70}
    Chain: "J"
      Number of atoms: 711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 711
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 4, 'TRANS': 77}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 3453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3453
          Classifications: {'peptide': 431}
          Link IDs: {'PTRANS': 20, 'TRANS': 410}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 3266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3266
          Classifications: {'peptide': 406}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 387}
          Chain breaks: 2
  Time building chain proxies: 1.84, per 1000 atoms: 0.23
  Number of scatterers: 8029
  At special positions: 0
  Unit cell: (121.8, 127.4, 100.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1528      8.00
     N    1346      7.00
     C    5124      6.00
    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: 0.48
  Conformation dependent library (CDL) restraints added in 404.8 milliseconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 12 sheets defined
      47.9% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'H' and resid 588 through 656
      removed outlier: 3.871A  pdb=" N   LYS H 597 " --> pdb=" O   LYS H 593 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS H 622 " --> pdb=" O   ARG H 618 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LYS H 623 " --> pdb=" O   ARG H 619 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN H 624 " --> pdb=" O   GLN H 620 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE H 629 " --> pdb=" O   LYS H 625 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU H 633 " --> pdb=" O   PHE H 629 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ILE H 634 " --> pdb=" O   GLY H 630 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   ALA H 635 " --> pdb=" O   HIS H 631 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR H 636 " --> pdb=" O   ARG H 632 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU H 641 " --> pdb=" O   HIS H 637 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG H 642 " --> pdb=" O   THR H 638 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG H 647 " --> pdb=" O   ASP H 643 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 10
      removed outlier: 3.663A  pdb=" N   THR J   8 " --> pdb=" O   GLN J   4 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ALA J  10 " --> pdb=" O   LEU J   6 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 88 through 102
    Processing helix  chain 'K' and resid 50 through 59
      removed outlier: 3.714A  pdb=" N   ALA K  59 " --> pdb=" O   ILE K  55 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 82 through 93
      removed outlier: 3.739A  pdb=" N   THR K  93 " --> pdb=" O   TYR K  89 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 116 through 127
      removed outlier: 3.526A  pdb=" N   LEU K 120 " --> pdb=" O   ASP K 116 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ARG K 122 " --> pdb=" O   ALA K 118 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   TYR K 123 " --> pdb=" O   ILE K 119 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR K 124 " --> pdb=" O   LEU K 120 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 141 through 148
      removed outlier: 3.670A  pdb=" N   ALA K 146 " --> pdb=" O   PRO K 142 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 185 through 196
      removed outlier: 3.611A  pdb=" N   LEU K 189 " --> pdb=" O   GLY K 185 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 197 through 201
    Processing helix  chain 'K' and resid 203 through 210
      removed outlier: 3.966A  pdb=" N   ASN K 209 " --> pdb=" O   ASN K 205 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 215 through 227
      removed outlier: 4.196A  pdb=" N   ASP K 219 " --> pdb=" O   LYS K 215 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 227 through 235
    Processing helix  chain 'K' and resid 242 through 271
    Processing helix  chain 'K' and resid 282 through 285
    Processing helix  chain 'K' and resid 303 through 312
      removed outlier: 3.634A  pdb=" N   TYR K 312 " --> pdb=" O   GLN K 308 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 324 through 327
    Processing helix  chain 'K' and resid 328 through 342
    Processing helix  chain 'K' and resid 381 through 390
      removed outlier: 3.998A  pdb=" N   SER K 386 " --> pdb=" O   GLU K 382 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 397 through 401
      removed outlier: 3.841A  pdb=" N   LEU K 400 " --> pdb=" O   SER K 397 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 403 through 416
      removed outlier: 3.739A  pdb=" N   ARG K 407 " --> pdb=" O   GLY K 403 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE K 409 " --> pdb=" O   GLU K 405 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS K 410 " --> pdb=" O   GLN K 406 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ILE K 414 " --> pdb=" O   LYS K 410 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ARG K 415 " --> pdb=" O   GLU K 411 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 428 through 434
      removed outlier: 3.987A  pdb=" N   LYS K 433 " --> pdb=" O   MET K 429 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE K 434 " --> pdb=" O   MET K 430 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 434 through 445
    Processing helix  chain 'K' and resid 457 through 464
      removed outlier: 3.691A  pdb=" N   GLU K 461 " --> pdb=" O   LYS K 457 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR K 462 " --> pdb=" O   GLU K 458 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 57 through 61
      removed outlier: 3.565A  pdb=" N   LYS L  61 " --> pdb=" O   LYS L  58 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 77 through 98
      removed outlier: 3.502A  pdb=" N   ARG L  94 " --> pdb=" O   ILE L  90 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 100 through 105
      removed outlier: 4.116A  pdb=" N   ALA L 104 " --> pdb=" O   ASP L 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 134
      removed outlier: 3.699A  pdb=" N   LEU L 124 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLU L 125 " --> pdb=" O   GLN L 121 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE L 126 " --> pdb=" O   SER L 122 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN L 129 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 145 through 153
    Processing helix  chain 'L' and resid 181 through 184
      removed outlier: 3.982A  pdb=" N   VAL L 184 " --> pdb=" O   ASP L 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 181 through 184'
    Processing helix  chain 'L' and resid 191 through 202
      removed outlier: 4.296A  pdb=" N   ASN L 195 " --> pdb=" O   GLY L 191 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS L 200 " --> pdb=" O   ASP L 196 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU L 201 " --> pdb=" O   SER L 197 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 206 through 216
    Processing helix  chain 'L' and resid 223 through 228
    Processing helix  chain 'L' and resid 295 through 299
      removed outlier: 3.629A  pdb=" N   ARG L 298 " --> pdb=" O   GLY L 295 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 311 through 317
      removed outlier: 3.552A  pdb=" N   LEU L 315 " --> pdb=" O   ASN L 311 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 322 through 331
      removed outlier: 3.900A  pdb=" N   LYS L 327 " --> pdb=" O   ILE L 323 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ALA L 328 " --> pdb=" O   ASN L 324 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL L 329 " --> pdb=" O   LYS L 325 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU L 331 " --> pdb=" O   LYS L 327 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 339 through 342
      removed outlier: 3.661A  pdb=" N   ILE L 342 " --> pdb=" O   THR L 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 339 through 342'
    Processing helix  chain 'L' and resid 344 through 355
      removed outlier: 3.629A  pdb=" N   LEU L 349 " --> pdb=" O   PHE L 345 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LEU L 350 " --> pdb=" O   LYS L 346 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY L 351 " --> pdb=" O   GLU L 347 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 362 through 376
    Processing helix  chain 'L' and resid 427 through 441
      removed outlier: 3.950A  pdb=" N   GLY L 431 " --> pdb=" O   ILE L 427 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   THR L 441 " --> pdb=" O   LYS L 437 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 451 through 458
      removed outlier: 3.536A  pdb=" N   LYS L 457 " --> pdb=" O   LYS L 453 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 459 through 465
      removed outlier: 3.526A  pdb=" N   TRP L 463 " --> pdb=" O   ALA L 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 25 through 30
      removed outlier: 3.813A  pdb=" N   ASP J  28 " --> pdb=" O   THR J  62 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR J  60 " --> pdb=" O   TYR J  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 29 through 31
      removed outlier: 3.523A  pdb=" N   CYS K  29 " --> pdb=" O   ALA K  19 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA K  19 " --> pdb=" O   CYS K  29 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY K  20 " --> pdb=" O   VAL K   9 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   THR K 107 " --> pdb=" O   ILE K  10 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ASN K  12 " --> pdb=" O   THR K 107 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU K 104 " --> pdb=" O   GLN K 137 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   VAL K 139 " --> pdb=" O   LEU K 104 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE K 106 " --> pdb=" O   VAL K 139 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 44 through 48
      removed outlier: 3.737A  pdb=" N   GLU K  44 " --> pdb=" O   ASP K  40 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE K  36 " --> pdb=" O   ILE K  48 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR K  35 " --> pdb=" O   TYR K  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 173 through 174
      removed outlier: 6.248A  pdb=" N   PHE K 155 " --> pdb=" O   ILE K 393 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 287 through 291
      removed outlier: 3.529A  pdb=" N   LEU K 301 " --> pdb=" O   LYS K 288 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54
    Processing sheet with id=AA8, first strand: chain 'L' and resid 113 through 115
      removed outlier: 3.595A  pdb=" N   LEU L 143 " --> pdb=" O   LEU L 113 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR L 115 " --> pdb=" O   LEU L 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'L' and resid 139 through 140
      removed outlier: 3.938A  pdb=" N   LEU L 140 " --> pdb=" O   ILE L 449 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE L 449 " --> pdb=" O   LEU L 140 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'L' and resid 178 through 179
    Processing sheet with id=AB2, first strand: chain 'L' and resid 178 through 179
      removed outlier: 6.551A  pdb=" N   CYS L 160 " --> pdb=" O   ILE L 334 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   VAL L 336 " --> pdb=" O   CYS L 160 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE L 162 " --> pdb=" O   VAL L 336 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 282 through 285

    319 hydrogen bonds defined for protein.
    885 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: 1.23

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.01 -     1.20: 14
        1.20 -     1.39: 3199
        1.39 -     1.58: 4917
        1.58 -     1.77: 14
        1.77 -     1.96: 45
  Bond restraints: 8189
  Sorted by residual:
  bond pdb=" SD  MET H 608 "
       pdb=" CE  MET H 608 "
    ideal  model  delta    sigma   weight residual
    1.791  1.293  0.498 2.50e-02 1.60e+03 3.96e+02
  bond pdb=" CZ  TYR K  91 "
       pdb=" OH  TYR K  91 "
    ideal  model  delta    sigma   weight residual
    1.376  1.061  0.315 2.10e-02 2.27e+03 2.25e+02
  bond pdb=" CA  GLU H 590 "
       pdb=" C   GLU H 590 "
    ideal  model  delta    sigma   weight residual
    1.523  1.723 -0.200 1.34e-02 5.57e+03 2.23e+02
  bond pdb=" CG  LEU H 594 "
       pdb=" CD2 LEU H 594 "
    ideal  model  delta    sigma   weight residual
    1.521  1.960 -0.439 3.30e-02 9.18e+02 1.77e+02
  bond pdb=" CD  GLU H 595 "
       pdb=" OE2 GLU H 595 "
    ideal  model  delta    sigma   weight residual
    1.249  1.010  0.239 1.90e-02 2.77e+03 1.59e+02
  ... (remaining 8184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.16: 11038
       13.16 -    26.33: 16
       26.33 -    39.49: 4
       39.49 -    52.65: 2
       52.65 -    65.82: 1
  Bond angle restraints: 11061
  Sorted by residual:
  angle pdb=" CA  GLU H 590 "
        pdb=" CB  GLU H 590 "
        pdb=" CG  GLU H 590 "
      ideal   model   delta    sigma   weight residual
     114.10  179.92  -65.82 2.00e+00 2.50e-01 1.08e+03
  angle pdb=" N   GLU H 590 "
        pdb=" CA  GLU H 590 "
        pdb=" CB  GLU H 590 "
      ideal   model   delta    sigma   weight residual
     110.49  158.68  -48.19 1.69e+00 3.50e-01 8.13e+02
  angle pdb=" CE1 TYR K  91 "
        pdb=" CZ  TYR K  91 "
        pdb=" OH  TYR K  91 "
      ideal   model   delta    sigma   weight residual
     119.90   75.29   44.61 3.00e+00 1.11e-01 2.21e+02
  angle pdb=" C   GLU H 590 "
        pdb=" CA  GLU H 590 "
        pdb=" CB  GLU H 590 "
      ideal   model   delta    sigma   weight residual
     110.42   81.97   28.45 1.99e+00 2.53e-01 2.04e+02
  angle pdb=" CB  LEU H 594 "
        pdb=" CG  LEU H 594 "
        pdb=" CD2 LEU H 594 "
      ideal   model   delta    sigma   weight residual
     110.70   74.19   36.51 3.00e+00 1.11e-01 1.48e+02
  ... (remaining 11056 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4498
       17.76 -    35.52: 395
       35.52 -    53.28: 85
       53.28 -    71.04: 22
       71.04 -    88.80: 10
  Dihedral angle restraints: 5010
    sinusoidal: 2093
      harmonic: 2917
  Sorted by residual:
  dihedral pdb=" C   GLU H 590 "
           pdb=" N   GLU H 590 "
           pdb=" CA  GLU H 590 "
           pdb=" CB  GLU H 590 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -83.17  -39.43     0      2.50e+00 1.60e-01 2.49e+02
  dihedral pdb=" N   GLU H 590 "
           pdb=" C   GLU H 590 "
           pdb=" CA  GLU H 590 "
           pdb=" CB  GLU H 590 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.62  -35.82     0      2.50e+00 1.60e-01 2.05e+02
  dihedral pdb=" N   LEU H 592 "
           pdb=" C   LEU H 592 "
           pdb=" CA  LEU H 592 "
           pdb=" CB  LEU H 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  153.02  -30.22     0      2.50e+00 1.60e-01 1.46e+02
  ... (remaining 5007 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.265: 1213
       0.265 -    0.530: 7
       0.530 -    0.796: 1
       0.796 -    1.061: 2
       1.061 -    1.326: 3
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CA  LEU H 592 "
            pdb=" N   LEU H 592 "
            pdb=" C   LEU H 592 "
            pdb=" CB  LEU H 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.18    1.33 2.00e-01 2.50e+01 4.40e+01
  chirality pdb=" CA  GLU H 590 "
            pdb=" N   GLU H 590 "
            pdb=" C   GLU H 590 "
            pdb=" CB  GLU H 590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.18    1.33 2.00e-01 2.50e+01 4.39e+01
  chirality pdb=" CA  LEU H 594 "
            pdb=" N   LEU H 594 "
            pdb=" C   LEU H 594 "
            pdb=" CB  LEU H 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.40    1.11 2.00e-01 2.50e+01 3.07e+01
  ... (remaining 1223 not shown)

  Planarity restraints: 1415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H 590 "    0.085 2.00e-02 2.50e+03   1.61e-01 2.59e+02
        pdb=" CD  GLU H 590 "   -0.277 2.00e-02 2.50e+03
        pdb=" OE1 GLU H 590 "    0.122 2.00e-02 2.50e+03
        pdb=" OE2 GLU H 590 "    0.070 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K  91 "   -0.000 2.00e-02 2.50e+03   8.94e-02 1.60e+02
        pdb=" CG  TYR K  91 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR K  91 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR K  91 "    0.054 2.00e-02 2.50e+03
        pdb=" CE1 TYR K  91 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR K  91 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR K  91 "   -0.195 2.00e-02 2.50e+03
        pdb=" OH  TYR K  91 "    0.149 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER K  98 "    0.047 2.00e-02 2.50e+03   9.44e-02 8.92e+01
        pdb=" C   SER K  98 "   -0.163 2.00e-02 2.50e+03
        pdb=" O   SER K  98 "    0.061 2.00e-02 2.50e+03
        pdb=" N   PRO K  99 "    0.056 2.00e-02 2.50e+03
  ... (remaining 1412 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1838
        2.79 -     3.32: 7371
        3.32 -     3.85: 12341
        3.85 -     4.37: 13764
        4.37 -     4.90: 23711
  Nonbonded interactions: 59025
  Sorted by model distance:
  nonbonded pdb=" O   THR K 390 "
            pdb=" OG1 THR K 422 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLU K 262 "
            pdb=" NE2 GLN K 266 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   SER K 386 "
            pdb=" OG1 THR K 390 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   GLN K 230 "
            pdb=" OG1 THR K 234 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" CB  GLU K 195 "
            pdb=" OE1 GLU K 195 "
     model   vdw
     2.348 2.752
  ... (remaining 59020 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.180
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
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      :  0.016   0.498   8189  Z= 0.690
  Angle     :  1.717  65.818  11061  Z= 0.840
  Chirality :  0.098   1.326   1226
  Planarity :  0.010   0.161   1415
  Dihedral  : 14.728  88.801   3114
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.52 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -2.52 (0.24), residues: 974
  helix: -1.44 (0.22), residues: 414
  sheet: -1.10 (0.43), residues: 122
  loop : -1.98 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.044   0.002   ARG J  89 
 TYR   0.195   0.005   TYR K  91 
 PHE   0.053   0.003   PHE L 440 
 TRP   0.116   0.004   TRP K 227 
 HIS   0.087   0.005   HIS L  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01635 /  0.69 ( 8189)
  covalent geometry    : angle       1.71658 /  0.84 (11061)
  hydrogen bonds       : bond        0.20192 / 13.39 (  317)
  hydrogen bonds       : angle       6.69275 /  4.82 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  627 LEU cc_start: 0.7029 (mm) cc_final: 0.6696 (mt)
REVERT: J   61 LYS cc_start: 0.3070 (ttmm) cc_final: 0.2764 (mttt)
REVERT: J   97 MET cc_start: 0.0549 (mpp) cc_final: 0.0028 (ptt)
REVERT: K   85 MET cc_start: 0.7694 (mmp) cc_final: 0.7415 (mtt)
REVERT: K  147 LEU cc_start: 0.7526 (tt) cc_final: 0.7318 (tt)
REVERT: K  165 ASN cc_start: 0.8357 (m-40) cc_final: 0.8090 (m-40)
REVERT: K  176 LYS cc_start: 0.7666 (mptt) cc_final: 0.7176 (tttt)
REVERT: K  177 ASN cc_start: 0.6205 (m-40) cc_final: 0.5726 (m110)
REVERT: K  181 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7948 (mtt-85)
REVERT: K  223 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6626 (mm-30)
REVERT: K  243 LEU cc_start: 0.6819 (mp) cc_final: 0.6503 (mt)
REVERT: K  455 TYR cc_start: 0.7095 (m-80) cc_final: 0.6828 (m-80)
REVERT: K  459 ASP cc_start: 0.6264 (m-30) cc_final: 0.6006 (p0)
REVERT: L  153 MET cc_start: 0.7751 (tpt) cc_final: 0.7392 (tpp)
REVERT: L  307 LYS cc_start: 0.6530 (mmmt) cc_final: 0.5665 (mtpt)
REVERT: L  356 ASP cc_start: 0.7419 (t0) cc_final: 0.7078 (t0)
REVERT: L  439 ILE cc_start: 0.7037 (tp) cc_final: 0.6720 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0955
  time to fit residues: 24.6917
Evaluate side-chains
  124 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45]
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 209 ASN
K 266 GLN
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  69 GLN
L 402 GLN
L 433 GLN
L 466 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.210639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.198907 restraints weight = 9279.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.173988 restraints weight = 16311.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.171033 restraints weight = 15594.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.171526 restraints weight = 15217.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.172104 restraints weight = 11766.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8189  Z= 0.128
  Angle     :  0.607   8.466  11061  Z= 0.317
  Chirality :  0.045   0.202   1226
  Planarity :  0.005   0.062   1415
  Dihedral  :  5.318  59.633   1061
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.44 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  8.39 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.70 (0.26), residues: 974
  helix: -0.45 (0.25), residues: 409
  sheet: -0.93 (0.45), residues: 116
  loop : -1.80 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 632 
 TYR   0.012   0.001   TYR K  89 
 PHE   0.032   0.001   PHE K 191 
 TRP   0.010   0.001   TRP K 227 
 HIS   0.004   0.001   HIS L  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 8189)
  covalent geometry    : angle       0.60748 /  0.32 (11061)
  hydrogen bonds       : bond        0.04607 /  3.13 (  317)
  hydrogen bonds       : angle       4.88839 /  3.50 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  627 LEU cc_start: 0.8052 (mm) cc_final: 0.7680 (mt)
REVERT: J   97 MET cc_start: 0.0719 (mpp) cc_final: 0.0113 (ptt)
REVERT: K    5 ARG cc_start: 0.6664 (mpt180) cc_final: 0.5910 (tpp-160)
REVERT: K   90 LEU cc_start: 0.7813 (mt) cc_final: 0.7528 (mp)
REVERT: K  124 TYR cc_start: 0.7205 (m-80) cc_final: 0.6991 (m-80)
REVERT: K  176 LYS cc_start: 0.7682 (mptt) cc_final: 0.7329 (ptmt)
REVERT: K  177 ASN cc_start: 0.5858 (m-40) cc_final: 0.5580 (m110)
REVERT: K  181 ARG cc_start: 0.8615 (mtt90) cc_final: 0.8327 (mtt-85)
REVERT: K  223 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6601 (mm-30)
REVERT: K  329 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.4419 (tp)
  outliers start: 19
  outliers final: 11
  residues processed: 151
  average time/residue: 0.0932
  time to fit residues: 18.6766
Evaluate side-chains
  137 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  180 VAL
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  360 ILE
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [46, 73, 38, 72, 32, 29, 89, 39, 42, 67, 37]
   chunk 46 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0770
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  54 HIS
L 352 GLN
L 402 GLN
L 466 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.209661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196842 restraints weight = 9141.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.172328 restraints weight = 16897.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.170209 restraints weight = 14174.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.170895 restraints weight = 12207.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.170991 restraints weight = 9902.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8189  Z= 0.110
  Angle     :  0.570   7.254  11061  Z= 0.297
  Chirality :  0.043   0.210   1226
  Planarity :  0.004   0.056   1415
  Dihedral  :  4.922  54.148   1061
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.34 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.30 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.39 (0.27), residues: 974
  helix: -0.06 (0.26), residues: 421
  sheet: -1.04 (0.44), residues: 128
  loop : -1.73 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 632 
 TYR   0.012   0.001   TYR J  27 
 PHE   0.026   0.001   PHE K 191 
 TRP   0.006   0.001   TRP K 454 
 HIS   0.004   0.001   HIS L 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 8189)
  covalent geometry    : angle       0.56987 /  0.30 (11061)
  hydrogen bonds       : bond        0.03977 /  2.69 (  317)
  hydrogen bonds       : angle       4.50824 /  3.22 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: J   25 TRP cc_start: 0.7157 (m100) cc_final: 0.5859 (m100)
REVERT: J   97 MET cc_start: 0.0607 (mpp) cc_final: 0.0042 (ptt)
REVERT: K    4 ASN cc_start: 0.6625 (t0) cc_final: 0.6376 (t0)
REVERT: K    5 ARG cc_start: 0.6939 (mpt180) cc_final: 0.6256 (tpp-160)
REVERT: K  158 ASP cc_start: 0.8680 (t70) cc_final: 0.8389 (p0)
REVERT: K  176 LYS cc_start: 0.7785 (mptt) cc_final: 0.7564 (tttt)
REVERT: K  177 ASN cc_start: 0.6386 (m-40) cc_final: 0.6046 (m110)
REVERT: K  181 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8291 (ttm-80)
REVERT: K  311 GLU cc_start: 0.6030 (tp30) cc_final: 0.5720 (tp30)
REVERT: K  329 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.4482 (tp)
REVERT: K  459 ASP cc_start: 0.7369 (p0) cc_final: 0.7165 (p0)
REVERT: L   43 ARG cc_start: 0.7158 (ttt90) cc_final: 0.6823 (ttt-90)
REVERT: L   47 GLN cc_start: 0.7704 (tt0) cc_final: 0.7407 (pt0)
REVERT: L  319 ASN cc_start: 0.7366 (t0) cc_final: 0.7164 (m-40)
  outliers start: 18
  outliers final: 9
  residues processed: 142
  average time/residue: 0.0934
  time to fit residues: 17.9648
Evaluate side-chains
  129 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [39, 84, 64, 63, 2, 67, 49, 71, 37, 53, 25]
   chunk 39 optimal weight:    0.0770
   chunk 84 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.1340

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 157 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.191522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.183545 restraints weight = 10128.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.151324 restraints weight = 19516.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.151475 restraints weight = 18895.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.151237 restraints weight = 17092.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.151287 restraints weight = 15852.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8189  Z= 0.122
  Angle     :  0.573   7.311  11061  Z= 0.299
  Chirality :  0.043   0.200   1226
  Planarity :  0.004   0.054   1415
  Dihedral  :  4.815  51.231   1061
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.85 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.76 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.25 (0.27), residues: 974
  helix:  0.17 (0.26), residues: 422
  sheet: -0.98 (0.45), residues: 128
  loop : -1.79 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 632 
 TYR   0.013   0.001   TYR L 177 
 PHE   0.022   0.001   PHE K 191 
 TRP   0.007   0.001   TRP K 449 
 HIS   0.006   0.001   HIS L 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 8189)
  covalent geometry    : angle       0.57317 /  0.30 (11061)
  hydrogen bonds       : bond        0.04052 /  2.74 (  317)
  hydrogen bonds       : angle       4.37972 /  3.12 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: J   25 TRP cc_start: 0.7185 (m100) cc_final: 0.5921 (m100)
REVERT: J   97 MET cc_start: 0.0585 (mpp) cc_final: 0.0025 (ptt)
REVERT: K    5 ARG cc_start: 0.7114 (mpt180) cc_final: 0.6489 (tpp-160)
REVERT: K   54 MET cc_start: 0.6760 (mtt) cc_final: 0.6225 (mtp)
REVERT: K  176 LYS cc_start: 0.7926 (mptt) cc_final: 0.7564 (ptmt)
REVERT: K  177 ASN cc_start: 0.6151 (m-40) cc_final: 0.5942 (m110)
REVERT: K  223 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6936 (mm-30)
REVERT: K  311 GLU cc_start: 0.6171 (tp30) cc_final: 0.5957 (tp30)
REVERT: L   43 ARG cc_start: 0.7092 (ttt90) cc_final: 0.6801 (ttt-90)
REVERT: L   47 GLN cc_start: 0.7770 (tt0) cc_final: 0.7461 (pt0)
REVERT: L  465 VAL cc_start: 0.8442 (t) cc_final: 0.8222 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 135
  average time/residue: 0.0953
  time to fit residues: 17.1321
Evaluate side-chains
  122 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain L residue   88 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  333 ILE
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [48, 4, 39, 13, 53, 62, 49, 12, 58, 6, 34]
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0370
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.3862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   4 ASN
K 308 GLN
L  98 ASN
L 402 GLN
L 466 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.189345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.175376 restraints weight = 9830.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.155499 restraints weight = 19082.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152506 restraints weight = 17217.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152801 restraints weight = 17437.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152716 restraints weight = 15499.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8189  Z= 0.135
  Angle     :  0.607  12.778  11061  Z= 0.313
  Chirality :  0.044   0.166   1226
  Planarity :  0.004   0.053   1415
  Dihedral  :  4.892  54.979   1061
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.67 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.43 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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 (0.27), residues: 974
  helix:  0.27 (0.26), residues: 424
  sheet: -0.91 (0.46), residues: 120
  loop : -1.87 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 632 
 TYR   0.015   0.001   TYR K 307 
 PHE   0.020   0.001   PHE K 191 
 TRP   0.006   0.001   TRP K 449 
 HIS   0.004   0.001   HIS K 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 ( 8189)
  covalent geometry    : angle       0.60720 /  0.31 (11061)
  hydrogen bonds       : bond        0.04097 /  2.75 (  317)
  hydrogen bonds       : angle       4.39727 /  3.13 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  594 LEU cc_start: 0.7023 (pt) cc_final: 0.6387 (tp)
REVERT: J   25 TRP cc_start: 0.7464 (m100) cc_final: 0.6126 (m100)
REVERT: J   97 MET cc_start: 0.0660 (mpp) cc_final: 0.0128 (ptt)
REVERT: K    5 ARG cc_start: 0.7184 (mpt180) cc_final: 0.6607 (tpp-160)
REVERT: K   54 MET cc_start: 0.6866 (mtt) cc_final: 0.6397 (mtp)
REVERT: K   91 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6008 (t80)
REVERT: K  223 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6644 (mm-30)
REVERT: K  339 LYS cc_start: 0.8129 (tppt) cc_final: 0.7584 (mmtp)
REVERT: L   43 ARG cc_start: 0.7225 (ttt90) cc_final: 0.6860 (ttt-90)
  outliers start: 26
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0880
  time to fit residues: 18.1479
Evaluate side-chains
  135 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain K residue  234 THR
Chi-restraints excluded: chain K residue  318 LEU
Chi-restraints excluded: chain L residue   88 VAL
Chi-restraints excluded: chain L residue   89 SER
Chi-restraints excluded: chain L residue   91 LEU
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  161 ILE
Chi-restraints excluded: chain L residue  309 ILE
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [18, 44, 23, 60, 95, 38, 1, 75, 36, 87, 73]
   chunk 18 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   4 ASN
K 177 ASN
** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 402 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.188915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.180619 restraints weight = 9918.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.150132 restraints weight = 17937.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149712 restraints weight = 18151.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149802 restraints weight = 14434.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.149821 restraints weight = 13432.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8189  Z= 0.108
  Angle     :  0.577   9.936  11061  Z= 0.296
  Chirality :  0.043   0.248   1226
  Planarity :  0.004   0.052   1415
  Dihedral  :  4.725  54.197   1061
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.44 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.66 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.02 (0.27), residues: 974
  helix:  0.42 (0.26), residues: 428
  sheet: -0.90 (0.45), residues: 126
  loop : -1.74 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 632 
 TYR   0.017   0.001   TYR K 307 
 PHE   0.019   0.001   PHE K 191 
 TRP   0.006   0.001   TRP L 330 
 HIS   0.003   0.001   HIS K 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 8189)
  covalent geometry    : angle       0.57728 /  0.30 (11061)
  hydrogen bonds       : bond        0.03565 /  2.41 (  317)
  hydrogen bonds       : angle       4.21933 /  2.99 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  594 LEU cc_start: 0.7569 (pt) cc_final: 0.6660 (tp)
REVERT: J   25 TRP cc_start: 0.7337 (m100) cc_final: 0.5921 (m100)
REVERT: J   84 LEU cc_start: 0.6950 (tt) cc_final: 0.6748 (tt)
REVERT: J   97 MET cc_start: 0.0497 (mpp) cc_final: 0.0023 (ptt)
REVERT: K    1 MET cc_start: 0.1995 (mmt) cc_final: 0.1754 (mmm)
REVERT: K    5 ARG cc_start: 0.7126 (mpt180) cc_final: 0.6765 (tpp-160)
REVERT: K   54 MET cc_start: 0.6757 (mtt) cc_final: 0.6200 (ttm)
REVERT: K   91 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.5896 (t80)
REVERT: K  176 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7771 (ptmt)
REVERT: K  223 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6614 (mm-30)
REVERT: K  339 LYS cc_start: 0.8090 (tppt) cc_final: 0.7501 (mmtp)
REVERT: L   43 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6610 (ttt-90)
  outliers start: 22
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0890
  time to fit residues: 17.1643
Evaluate side-chains
  134 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain J residue   14 SER
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  124 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  218 THR
Chi-restraints excluded: chain K residue  318 LEU
Chi-restraints excluded: chain L residue   89 SER
Chi-restraints excluded: chain L residue   91 LEU
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [55, 56, 6, 77, 36, 2, 76, 72, 16, 87, 40]
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0470
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.9682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   4 ASN
** K  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 177 ASN
** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 402 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.191579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.176450 restraints weight = 9648.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155665 restraints weight = 17467.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.152661 restraints weight = 18242.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152821 restraints weight = 20411.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153230 restraints weight = 16097.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8189  Z= 0.113
  Angle     :  0.587  10.648  11061  Z= 0.298
  Chirality :  0.043   0.228   1226
  Planarity :  0.004   0.049   1415
  Dihedral  :  4.676  55.182   1061
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.06 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.11 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.27), residues: 974
  helix:  0.53 (0.27), residues: 427
  sheet: -0.99 (0.44), residues: 135
  loop : -1.74 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 196 
 TYR   0.013   0.001   TYR J  27 
 PHE   0.018   0.001   PHE K 191 
 TRP   0.007   0.001   TRP K 449 
 HIS   0.003   0.001   HIS K 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 8189)
  covalent geometry    : angle       0.58650 /  0.30 (11061)
  hydrogen bonds       : bond        0.03609 /  2.42 (  317)
  hydrogen bonds       : angle       4.13538 /  2.94 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: J   25 TRP cc_start: 0.7354 (m100) cc_final: 0.6061 (m100)
REVERT: J   84 LEU cc_start: 0.7116 (tt) cc_final: 0.6913 (tt)
REVERT: J   97 MET cc_start: 0.0812 (mpp) cc_final: 0.0298 (ptt)
REVERT: K    1 MET cc_start: 0.2533 (mmt) cc_final: 0.2242 (mmm)
REVERT: K    5 ARG cc_start: 0.7146 (mpt180) cc_final: 0.6846 (tpp-160)
REVERT: K   54 MET cc_start: 0.6808 (mtt) cc_final: 0.6372 (mtp)
REVERT: K   91 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.5862 (t80)
REVERT: K  176 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7912 (ptmt)
REVERT: K  223 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6566 (mm-30)
REVERT: K  339 LYS cc_start: 0.8239 (tppt) cc_final: 0.7654 (mmtp)
REVERT: L   43 ARG cc_start: 0.7087 (ttt90) cc_final: 0.6717 (ttt-90)
  outliers start: 27
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0864
  time to fit residues: 17.0476
Evaluate side-chains
  141 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain J residue   14 SER
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  124 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  218 THR
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain K residue  318 LEU
Chi-restraints excluded: chain L residue   73 ILE
Chi-restraints excluded: chain L residue   89 SER
Chi-restraints excluded: chain L residue   91 LEU
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [24, 48, 45, 22, 28, 52, 8, 80, 26, 95, 68]
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 615 GLN
K   4 ASN
K 177 ASN
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 402 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.186293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.178325 restraints weight = 9755.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149973 restraints weight = 16825.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.149376 restraints weight = 19339.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149431 restraints weight = 17372.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149462 restraints weight = 15388.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8189  Z= 0.133
  Angle     :  0.615  13.545  11061  Z= 0.311
  Chirality :  0.044   0.218   1226
  Planarity :  0.004   0.051   1415
  Dihedral  :  4.817  58.332   1061
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.47 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.77 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.01 (0.27), residues: 974
  helix:  0.51 (0.27), residues: 426
  sheet: -0.99 (0.44), residues: 131
  loop : -1.80 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 632 
 TYR   0.016   0.002   TYR L 400 
 PHE   0.018   0.002   PHE K 191 
 TRP   0.008   0.001   TRP K 449 
 HIS   0.004   0.001   HIS K 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 ( 8189)
  covalent geometry    : angle       0.61532 /  0.31 (11061)
  hydrogen bonds       : bond        0.04000 /  2.69 (  317)
  hydrogen bonds       : angle       4.24888 /  3.02 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: H  594 LEU cc_start: 0.8008 (pt) cc_final: 0.7212 (tp)
REVERT: J   25 TRP cc_start: 0.7473 (m100) cc_final: 0.6284 (m100)
REVERT: J   76 GLU cc_start: 0.6062 (pm20) cc_final: 0.5740 (pm20)
REVERT: J   97 MET cc_start: 0.0658 (mpp) cc_final: 0.0125 (ptt)
REVERT: K    1 MET cc_start: 0.2335 (mmt) cc_final: 0.2106 (mmm)
REVERT: K   54 MET cc_start: 0.6979 (mtt) cc_final: 0.6543 (mtp)
REVERT: K   91 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6017 (t80)
REVERT: K  176 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8005 (ptmt)
REVERT: K  223 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6839 (mm-30)
REVERT: K  339 LYS cc_start: 0.8210 (tppt) cc_final: 0.7623 (mmtp)
REVERT: L   43 ARG cc_start: 0.6915 (ttt90) cc_final: 0.6495 (ttt-90)
  outliers start: 26
  outliers final: 21
  residues processed: 148
  average time/residue: 0.0850
  time to fit residues: 17.4004
Evaluate side-chains
  146 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain J residue   14 SER
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  124 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  169 ILE
Chi-restraints excluded: chain K residue  179 VAL
Chi-restraints excluded: chain K residue  218 THR
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain K residue  234 THR
Chi-restraints excluded: chain K residue  318 LEU
Chi-restraints excluded: chain K residue  412 LEU
Chi-restraints excluded: chain L residue   73 ILE
Chi-restraints excluded: chain L residue   88 VAL
Chi-restraints excluded: chain L residue   89 SER
Chi-restraints excluded: chain L residue   91 LEU
Chi-restraints excluded: chain L residue  161 ILE
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [22, 17, 63, 88, 14, 38, 30, 16, 86, 53, 65]
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 88 optimal weight:    0.0270
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0870
   overall best weight:    0.5016

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K   4 ASN
** K 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.188506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.180918 restraints weight = 10110.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.150176 restraints weight = 18453.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.148798 restraints weight = 22677.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149310 restraints weight = 20332.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149638 restraints weight = 15660.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8189  Z= 0.104
  Angle     :  0.587  13.938  11061  Z= 0.296
  Chirality :  0.043   0.218   1226
  Planarity :  0.004   0.050   1415
  Dihedral  :  4.589  55.398   1061
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.24 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.11 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.28), residues: 974
  helix:  0.64 (0.27), residues: 426
  sheet: -0.67 (0.46), residues: 122
  loop : -1.63 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 196 
 TYR   0.019   0.001   TYR L 400 
 PHE   0.024   0.001   PHE K 188 
 TRP   0.008   0.001   TRP K 227 
 HIS   0.002   0.001   HIS L 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 ( 8189)
  covalent geometry    : angle       0.58660 /  0.30 (11061)
  hydrogen bonds       : bond        0.03366 /  2.27 (  317)
  hydrogen bonds       : angle       4.12505 /  2.93 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  594 LEU cc_start: 0.8043 (pt) cc_final: 0.7292 (tp)
REVERT: J   25 TRP cc_start: 0.7361 (m100) cc_final: 0.6167 (m100)
REVERT: J   76 GLU cc_start: 0.6088 (pm20) cc_final: 0.5720 (pm20)
REVERT: J   97 MET cc_start: 0.0557 (mpp) cc_final: 0.0048 (ptt)
REVERT: K    1 MET cc_start: 0.2586 (mmt) cc_final: 0.2173 (mmm)
REVERT: K   54 MET cc_start: 0.6767 (mtt) cc_final: 0.6323 (mtp)
REVERT: K   91 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.5900 (t80)
REVERT: K  176 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7930 (ptmt)
REVERT: K  339 LYS cc_start: 0.8196 (tppt) cc_final: 0.7582 (mmtp)
REVERT: L   43 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6588 (ttt-90)
  outliers start: 19
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0866
  time to fit residues: 17.2956
Evaluate side-chains
  134 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain J residue   14 SER
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  124 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain L residue   73 ILE
Chi-restraints excluded: chain L residue   89 SER
Chi-restraints excluded: chain L residue   91 LEU
Chi-restraints excluded: chain L residue  315 LEU
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [77, 83, 11, 8, 40, 44, 14, 4, 53, 57, 2]
   chunk 77 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K   4 ASN
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 139 ASN
L 182 HIS
L 402 GLN
L 442 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.188519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.175839 restraints weight = 9451.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.155584 restraints weight = 18737.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.150824 restraints weight = 16962.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.150518 restraints weight = 15690.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150659 restraints weight = 14290.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8189  Z= 0.180
  Angle     :  0.674  12.298  11061  Z= 0.345
  Chirality :  0.046   0.216   1226
  Planarity :  0.005   0.075   1415
  Dihedral  :  5.091  62.418   1061
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.91 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.23 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.02 (0.27), residues: 974
  helix:  0.53 (0.27), residues: 418
  sheet: -1.08 (0.45), residues: 129
  loop : -1.76 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG K 196 
 TYR   0.023   0.002   TYR L 400 
 PHE   0.023   0.002   PHE K 244 
 TRP   0.008   0.002   TRP K 449 
 HIS   0.005   0.001   HIS K 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.18 ( 8189)
  covalent geometry    : angle       0.67404 /  0.34 (11061)
  hydrogen bonds       : bond        0.04773 /  3.21 (  317)
  hydrogen bonds       : angle       4.47906 /  3.21 (  885)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   25 TRP cc_start: 0.7578 (m100) cc_final: 0.6514 (m100)
REVERT: J   76 GLU cc_start: 0.6220 (pm20) cc_final: 0.5884 (pm20)
REVERT: J   97 MET cc_start: 0.0545 (mpp) cc_final: 0.0042 (ptt)
REVERT: K    1 MET cc_start: 0.3042 (mmt) cc_final: 0.2637 (mmm)
REVERT: K   54 MET cc_start: 0.7104 (mtt) cc_final: 0.6669 (mtp)
REVERT: K   91 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.6404 (t80)
REVERT: K  176 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8089 (ptmt)
REVERT: K  223 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6893 (mt-10)
REVERT: K  339 LYS cc_start: 0.8284 (tppt) cc_final: 0.7688 (mmtp)
REVERT: L   43 ARG cc_start: 0.7004 (ttt90) cc_final: 0.6612 (ttt-90)
  outliers start: 18
  outliers final: 12
  residues processed: 147
  average time/residue: 0.0866
  time to fit residues: 17.5914
Evaluate side-chains
  139 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  627 LEU
Chi-restraints excluded: chain J residue   14 SER
Chi-restraints excluded: chain K residue    7 CYS
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   91 TYR
Chi-restraints excluded: chain K residue  124 TYR
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  218 THR
Chi-restraints excluded: chain L residue   73 ILE
Chi-restraints excluded: chain L residue   88 VAL
Chi-restraints excluded: chain L residue  161 ILE
Chi-restraints excluded: chain L residue  402 GLN
Chi-restraints excluded: chain L residue  445 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks: [3, 59, 4, 36, 93, 55, 49, 16, 81, 94, 45]
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0000
   chunk 55 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 81 optimal weight:    0.4980
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K   4 ASN
K 317 GLN
** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 402 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.187625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.179626 restraints weight = 9754.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.152841 restraints weight = 17549.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151551 restraints weight = 20519.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.151687 restraints weight = 16527.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.151913 restraints weight = 14162.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8189  Z= 0.110
  Angle     :  0.602  13.550  11061  Z= 0.305
  Chirality :  0.043   0.218   1226
  Planarity :  0.004   0.060   1415
  Dihedral  :  4.603  56.383   1061
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.44 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.34 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.28), residues: 974
  helix:  0.72 (0.27), residues: 421
  sheet: -0.65 (0.46), residues: 127
  loop : -1.59 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 248 
 TYR   0.020   0.001   TYR L 400 
 PHE   0.022   0.001   PHE K 188 
 TRP   0.010   0.001   TRP K 227 
 HIS   0.003   0.001   HIS L 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 8189)
  covalent geometry    : angle       0.60155 /  0.31 (11061)
  hydrogen bonds       : bond        0.03572 /  2.40 (  317)
  hydrogen bonds       : angle       4.16414 /  2.96 (  885)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1321.28 seconds
wall clock time: 23 minutes 25.48 seconds (1405.48 seconds total)