Starting phenix.real_space_refine
on Thu Jul  2 16:07:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yqp_73343/07_2026/9yqp_73343.map"
  }
  resolution = 4.1
  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=   0.030
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      34      5.16       5
     C    5719      2.51       5
     N    1493      2.21       5
     O    1710      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8956
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1166
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 145}
    Chain: "B"
      Number of atoms: 7790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 970, 7790
          Classifications: {'peptide': 970}
          Link IDs: {'PTRANS': 33, 'TRANS': 936}
          Chain breaks: 7
  Time building chain proxies: 1.93, per 1000 atoms: 0.22
  Number of scatterers: 8956
  At special positions: 0
  Unit cell: (95.408, 105.376, 142.4, 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      34     16.00
     O    1710      8.00
     N    1493      7.00
     C    5719      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: 0.86
  Conformation dependent library (CDL) restraints added in 314.9 milliseconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2150

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 4 sheets defined
      36.4% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 20
    Processing helix  chain 'A' and resid 30 through 40
      removed outlier: 4.213A  pdb=" N   GLY A  34 " --> pdb=" O   THR A  30 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 81 through 94
    Processing helix  chain 'A' and resid 102 through 114
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 138 through 147
    Processing helix  chain 'B' and resid 3 through 17
      removed outlier: 3.984A  pdb=" N   ASP B  17 " --> pdb=" O   ARG B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 34
    Processing helix  chain 'B' and resid 70 through 74
      removed outlier: 3.529A  pdb=" N   LEU B  74 " --> pdb=" O   TRP B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.165A  pdb=" N   GLU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 173
    Processing helix  chain 'B' and resid 184 through 193
    Processing helix  chain 'B' and resid 271 through 281
    Processing helix  chain 'B' and resid 309 through 314
      removed outlier: 4.191A  pdb=" N   GLU B 312 " --> pdb=" O   PRO B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 355
    Processing helix  chain 'B' and resid 356 through 361
      removed outlier: 4.114A  pdb=" N   LYS B 359 " --> pdb=" O   PRO B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
      removed outlier: 3.952A  pdb=" N   LYS B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 391
    Processing helix  chain 'B' and resid 394 through 418
    Processing helix  chain 'B' and resid 423 through 436
      removed outlier: 3.895A  pdb=" N   LYS B 427 " --> pdb=" O   GLU B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 452
    Processing helix  chain 'B' and resid 637 through 649
      removed outlier: 3.663A  pdb=" N   VAL B 641 " --> pdb=" O   ASP B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 683
    Processing helix  chain 'B' and resid 704 through 706
      No H-bonds generated for 'chain 'B' and resid 704 through 706'
    Processing helix  chain 'B' and resid 742 through 744
      No H-bonds generated for 'chain 'B' and resid 742 through 744'
    Processing helix  chain 'B' and resid 818 through 832
      removed outlier: 3.597A  pdb=" N   ILE B 832 " --> pdb=" O   LEU B 828 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1028 through 1041
    Processing helix  chain 'B' and resid 1193 through 1206
    Processing helix  chain 'B' and resid 1207 through 1233
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29
    Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 42
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 35 through 42
    current: chain 'B' and resid 79 through 92
      removed outlier: 8.780A  pdb=" N   VAL B  80 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   ILE B 198 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 8.966A  pdb=" N   THR B  82 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 10.090A  pdb=" N   ASP B 200 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   GLU B  84 " --> pdb=" O   ASP B 200 " (cutoff:3.500A)
      removed outlier: 9.434A  pdb=" N   HIS B 202 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LEU B  86 " --> pdb=" O   HIS B 202 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LYS B 204 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU B  88 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLU B 206 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   VAL B  90 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLY B 223 " --> pdb=" O   ASP B 200 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS B 202 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   THR B 221 " --> pdb=" O   HIS B 202 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LYS B 204 " --> pdb=" O   GLY B 219 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   GLY B 219 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLU B 206 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   SER B 217 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   SER B 254 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU B 225 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU B 227 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ILE B 250 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ILE B 299 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   SER B 256 " --> pdb=" O   GLN B 297 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   GLN B 297 " --> pdb=" O   SER B 256 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   TYR B 258 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ILE B 295 " --> pdb=" O   TYR B 258 " (cutoff:3.500A)
      removed outlier: 9.976A  pdb=" N   TYR B 294 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   LEU B 333 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   PHE B 296 " --> pdb=" O   ILE B 331 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE B 331 " --> pdb=" O   PHE B 296 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   ILE B 329 " --> pdb=" O   PRO B 298 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   SER B 300 " --> pdb=" O   GLN B 327 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLN B 327 " --> pdb=" O   SER B 300 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   LEU B 320 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   THR B 533 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   CYS B 322 " --> pdb=" O   THR B 533 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LYS B 535 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE B 324 " --> pdb=" O   LYS B 535 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   VAL B 537 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   ILE B 326 " --> pdb=" O   VAL B 537 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   THR B 539 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ASN B 328 " --> pdb=" O   THR B 539 " (cutoff:3.500A)
      removed outlier: 9.649A  pdb=" N   VAL B 541 " --> pdb=" O   ASN B 328 " (cutoff:3.500A)
      removed outlier: 8.670A  pdb=" N   ALA B 330 " --> pdb=" O   VAL B 541 " (cutoff:3.500A)
      removed outlier: 9.507A  pdb=" N   ILE B 543 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   GLU B 332 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   HIS B 530 " --> pdb=" O   GLN B 566 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   SER B 538 " --> pdb=" O   ILE B 558 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ILE B 558 " --> pdb=" O   SER B 538 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   SER B 540 " --> pdb=" O   GLN B 556 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLN B 556 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   THR B 542 " --> pdb=" O   LYS B 554 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LYS B 554 " --> pdb=" O   THR B 542 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ARG B 544 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   ILE B 552 " --> pdb=" O   ARG B 544 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 572 through 579
    current: chain 'B' and resid 597 through 599
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 597 through 599
    current: chain 'B' and resid 623 through 628
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 623 through 628
    current: chain 'B' and resid 688 through 702
      removed outlier: 6.079A  pdb=" N   LEU B 690 " --> pdb=" O   SER B 725 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   GLY B 719 " --> pdb=" O   PRO B 696 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TYR B 698 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ASP B 717 " --> pdb=" O   TYR B 698 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 700 " --> pdb=" O   ILE B 715 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE B 715 " --> pdb=" O   VAL B 700 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU B 713 " --> pdb=" O   PRO B 702 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 746 through 753
    current: chain 'B' and resid 802 through 810
      removed outlier: 6.001A  pdb=" N   ASN B 910 " --> pdb=" O   ALA B 802 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASP B 952 " --> pdb=" O   ARG B 949 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   GLN B1014 " --> pdb=" O   ARG B1085 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   PHE B1087 " --> pdb=" O   GLN B1014 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL B1016 " --> pdb=" O   PHE B1087 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   LYS B1089 " --> pdb=" O   VAL B1016 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   VAL B1018 " --> pdb=" O   LYS B1089 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ASN B1091 " --> pdb=" O   VAL B1018 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   PHE B1020 " --> pdb=" O   ASN B1091 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   PHE B1093 " --> pdb=" O   PHE B1020 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA B1092 " --> pdb=" O   GLN B1110 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   GLN B1110 " --> pdb=" O   ALA B1092 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS B1094 " --> pdb=" O   LYS B1108 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LYS B1108 " --> pdb=" O   CYS B1094 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU B1112 " --> pdb=" O   LEU B1129 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B1129 " --> pdb=" O   LEU B1112 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   SER B1114 " --> pdb=" O   ALA B1127 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ALA B1127 " --> pdb=" O   SER B1114 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B1116 " --> pdb=" O   LEU B1125 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   LEU B1125 " --> pdb=" O   LEU B1116 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU B1118 " --> pdb=" O   GLN B1123 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   GLN B1123 " --> pdb=" O   LEU B1118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 813 through 816
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1147 through 1149

    404 hydrogen bonds defined for protein.
    1167 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: 1.55

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2250
        1.33 -     1.45: 1514
        1.45 -     1.57: 5272
        1.57 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 9097
  Sorted by residual:
  bond pdb=" N   GLN B 630 "
       pdb=" CA  GLN B 630 "
    ideal  model  delta    sigma   weight residual
    1.453  1.481 -0.027 9.20e-03 1.18e+04 8.82e+00
  bond pdb=" N   SER B 605 "
       pdb=" CA  SER B 605 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.15e-02 7.56e+03 8.13e+00
  bond pdb=" N   SER B 606 "
       pdb=" CA  SER B 606 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.033 1.27e-02 6.20e+03 6.57e+00
  bond pdb=" N   ASP B 602 "
       pdb=" CA  ASP B 602 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 1.31e-02 5.83e+03 6.54e+00
  bond pdb=" N   LEU B 608 "
       pdb=" CA  LEU B 608 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.42e+00
  ... (remaining 9092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11776
        1.41 -     2.82: 415
        2.82 -     4.23: 81
        4.23 -     5.64: 8
        5.64 -     7.05: 3
  Bond angle restraints: 12283
  Sorted by residual:
  angle pdb=" N   LEU B 587 "
        pdb=" CA  LEU B 587 "
        pdb=" C   LEU B 587 "
      ideal   model   delta    sigma   weight residual
     108.45  113.91   -5.46 1.26e+00 6.30e-01 1.87e+01
  angle pdb=" C   THR B 603 "
        pdb=" CA  THR B 603 "
        pdb=" CB  THR B 603 "
      ideal   model   delta    sigma   weight residual
     116.54  112.68    3.86 1.15e+00 7.56e-01 1.13e+01
  angle pdb=" N   LEU B 810 "
        pdb=" CA  LEU B 810 "
        pdb=" C   LEU B 810 "
      ideal   model   delta    sigma   weight residual
     108.66  101.61    7.05 2.16e+00 2.14e-01 1.06e+01
  angle pdb=" CA  GLY B 809 "
        pdb=" C   GLY B 809 "
        pdb=" O   GLY B 809 "
      ideal   model   delta    sigma   weight residual
     121.47  118.68    2.79 9.00e-01 1.23e+00 9.59e+00
  angle pdb=" CA  SER B 606 "
        pdb=" C   SER B 606 "
        pdb=" O   SER B 606 "
      ideal   model   delta    sigma   weight residual
     121.56  118.30    3.26 1.09e+00 8.42e-01 8.92e+00
  ... (remaining 12278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 5016
       17.31 -    34.63: 479
       34.63 -    51.94: 84
       51.94 -    69.26: 17
       69.26 -    86.57: 11
  Dihedral angle restraints: 5607
    sinusoidal: 2313
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" CA  ASP B 243 "
           pdb=" C   ASP B 243 "
           pdb=" N   LYS B 244 "
           pdb=" CA  LYS B 244 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ILE B  96 "
           pdb=" C   ILE B  96 "
           pdb=" N   LYS B  97 "
           pdb=" CA  LYS B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.12  -20.88     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  SER B 697 "
           pdb=" C   SER B 697 "
           pdb=" N   TYR B 698 "
           pdb=" CA  TYR B 698 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5604 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1182
       0.054 -    0.108: 180
       0.108 -    0.162: 68
       0.162 -    0.217: 2
       0.217 -    0.271: 2
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" CA  LEU B 810 "
            pdb=" N   LEU B 810 "
            pdb=" C   LEU B 810 "
            pdb=" CB  LEU B 810 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  VAL B  91 "
            pdb=" N   VAL B  91 "
            pdb=" C   VAL B  91 "
            pdb=" CB  VAL B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  VAL B 956 "
            pdb=" N   VAL B 956 "
            pdb=" C   VAL B 956 "
            pdb=" CB  VAL B 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.27e-01
  ... (remaining 1431 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 715 "   -0.016 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   ILE B 715 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ILE B 715 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 716 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  90 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.64e+00
        pdb=" C   VAL B  90 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   VAL B  90 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL B  91 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 629 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   SER B 629 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   SER B 629 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN B 630 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2690
        2.83 -     3.34: 8821
        3.34 -     3.86: 14423
        3.86 -     4.38: 16113
        4.38 -     4.90: 27621
  Nonbonded interactions: 69668
  Sorted by model distance:
  nonbonded pdb=" O   SER B 340 "
            pdb=" OD1 ASP B 343 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   GLU A 140 "
            pdb=" OE1 GLN A 144 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   GLU B 709 "
            pdb=" OE2 GLU B 765 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OH  TYR B 583 "
            pdb=" OD1 ASP B 602 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OE1 GLU B 765 "
            pdb=" O   LYS B 768 "
     model   vdw
     2.415 3.040
  ... (remaining 69663 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:             5.120
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.040
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5521
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      :  0.003   0.038   9097  Z= 0.189
  Angle     :  0.628   7.045  12283  Z= 0.367
  Chirality :  0.046   0.271   1434
  Planarity :  0.004   0.039   1556
  Dihedral  : 14.221  86.572   3457
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.27), residues: 1100
  helix:  1.40 (0.27), residues: 379
  sheet: -1.54 (0.28), residues: 345
  loop : -1.97 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 358 
 TYR   0.016   0.001   TYR B  98 
 PHE   0.022   0.002   PHE A  69 
 TRP   0.015   0.001   TRP B 374 
 HIS   0.006   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.19 ( 9097)
  covalent geometry    : angle       0.62828 /  0.37 (12283)
  hydrogen bonds       : bond        0.10099 /  5.72 (  404)
  hydrogen bonds       : angle       6.23148 /  4.45 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7303 (m-40) cc_final: 0.6929 (t0)
REVERT: B  204 LYS cc_start: 0.6592 (tttt) cc_final: 0.6234 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0815
  time to fit residues: 14.6353
Evaluate side-chains
  99 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 418 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5279 r_free = 0.5279 target = 0.330878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5227 r_free = 0.5227 target = 0.313024 restraints weight = 6832.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5223 r_free = 0.5223 target = 0.311497 restraints weight = 9702.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5222 r_free = 0.5222 target = 0.311432 restraints weight = 9885.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5221 r_free = 0.5221 target = 0.310999 restraints weight = 9350.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5220 r_free = 0.5220 target = 0.310764 restraints weight = 8997.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.5227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5529
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9097  Z= 0.125
  Angle     :  0.592   7.087  12283  Z= 0.311
  Chirality :  0.045   0.164   1434
  Planarity :  0.004   0.035   1556
  Dihedral  :  4.931  21.429   1183
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.08 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.27), residues: 1100
  helix:  1.53 (0.27), residues: 383
  sheet: -1.29 (0.29), residues: 346
  loop : -1.67 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 762 
 TYR   0.008   0.001   TYR B 306 
 PHE   0.013   0.002   PHE B 706 
 TRP   0.008   0.001   TRP B 393 
 HIS   0.008   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 9097)
  covalent geometry    : angle       0.59157 /  0.31 (12283)
  hydrogen bonds       : bond        0.03433 /  2.18 (  404)
  hydrogen bonds       : angle       5.01291 /  3.65 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7312 (tpp) cc_final: 0.7080 (mmt)
REVERT: A  146 MET cc_start: 0.5034 (mmm) cc_final: 0.4830 (mmm)
REVERT: B   40 ASN cc_start: 0.7443 (m-40) cc_final: 0.6961 (t0)
REVERT: B  204 LYS cc_start: 0.6717 (tttt) cc_final: 0.6489 (tttp)
REVERT: B  392 MET cc_start: 0.6118 (mpp) cc_final: 0.5500 (mtt)
REVERT: B  814 HIS cc_start: 0.8134 (t-170) cc_final: 0.7894 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0829
  time to fit residues: 14.9118
Evaluate side-chains
  99 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 93 optimal weight:    0.0370
   chunk 12 optimal weight:    0.2980
   chunk 85 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.3036

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1110 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5281 r_free = 0.5281 target = 0.330939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5229 r_free = 0.5229 target = 0.313302 restraints weight = 6811.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5228 r_free = 0.5228 target = 0.312465 restraints weight = 9613.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.311741 restraints weight = 9185.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.5224 r_free = 0.5224 target = 0.311185 restraints weight = 9173.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5223 r_free = 0.5223 target = 0.310922 restraints weight = 9004.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.5229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5518
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9097  Z= 0.123
  Angle     :  0.587   7.581  12283  Z= 0.306
  Chirality :  0.045   0.174   1434
  Planarity :  0.004   0.032   1556
  Dihedral  :  4.858  17.141   1183
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.66 (0.27), residues: 1100
  helix:  1.56 (0.26), residues: 385
  sheet: -1.33 (0.29), residues: 347
  loop : -1.57 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 762 
 TYR   0.031   0.001   TYR B 338 
 PHE   0.032   0.002   PHE A  69 
 TRP   0.009   0.001   TRP B 767 
 HIS   0.008   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 9097)
  covalent geometry    : angle       0.58698 /  0.31 (12283)
  hydrogen bonds       : bond        0.03182 /  2.03 (  404)
  hydrogen bonds       : angle       4.87004 /  3.55 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7416 (m-40) cc_final: 0.6946 (t0)
REVERT: B  392 MET cc_start: 0.6013 (mpp) cc_final: 0.4860 (mmm)
REVERT: B  814 HIS cc_start: 0.8048 (t-170) cc_final: 0.7836 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0811
  time to fit residues: 15.7837
Evaluate side-chains
  102 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 70 optimal weight:    0.2980
   chunk 71 optimal weight:    0.3980
   chunk 67 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.322114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.301720 restraints weight = 7055.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.301689 restraints weight = 11338.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.5183 r_free = 0.5183 target = 0.300730 restraints weight = 10692.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5183 r_free = 0.5183 target = 0.300648 restraints weight = 11614.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.5182 r_free = 0.5182 target = 0.300414 restraints weight = 10544.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.5100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9097  Z= 0.188
  Angle     :  0.685  10.169  12283  Z= 0.359
  Chirality :  0.048   0.297   1434
  Planarity :  0.004   0.039   1556
  Dihedral  :  5.283  24.723   1183
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.37 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.27), residues: 1100
  helix:  1.50 (0.26), residues: 386
  sheet: -1.76 (0.28), residues: 350
  loop : -1.70 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 567 
 TYR   0.021   0.002   TYR B 698 
 PHE   0.040   0.002   PHE B 721 
 TRP   0.033   0.002   TRP B 259 
 HIS   0.008   0.001   HIS B 530 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.19 ( 9097)
  covalent geometry    : angle       0.68485 /  0.36 (12283)
  hydrogen bonds       : bond        0.03326 /  2.18 (  404)
  hydrogen bonds       : angle       5.25360 /  3.80 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7467 (m-40) cc_final: 0.7001 (t0)
REVERT: B  392 MET cc_start: 0.6730 (mpp) cc_final: 0.5642 (mtt)
REVERT: B  698 TYR cc_start: 0.8239 (p90) cc_final: 0.7804 (p90)
REVERT: B  924 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7258 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 135
  average time/residue: 0.0714
  time to fit residues: 14.8071
Evaluate side-chains
  107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    0.2980
   chunk 89 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 99 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 814 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.324041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5204 r_free = 0.5204 target = 0.306230 restraints weight = 6949.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5201 r_free = 0.5201 target = 0.305012 restraints weight = 10469.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5198 r_free = 0.5198 target = 0.304356 restraints weight = 10262.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.5195 r_free = 0.5195 target = 0.303433 restraints weight = 10150.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.5193 r_free = 0.5193 target = 0.302833 restraints weight = 11042.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.5118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5642
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9097  Z= 0.167
  Angle     :  0.660   9.744  12283  Z= 0.347
  Chirality :  0.047   0.232   1434
  Planarity :  0.004   0.044   1556
  Dihedral  :  5.282  24.433   1183
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.88 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.27), residues: 1100
  helix:  1.47 (0.26), residues: 385
  sheet: -1.68 (0.29), residues: 345
  loop : -1.72 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 567 
 TYR   0.021   0.001   TYR B 258 
 PHE   0.038   0.002   PHE A  69 
 TRP   0.028   0.002   TRP B 259 
 HIS   0.009   0.001   HIS B 530 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.17 ( 9097)
  covalent geometry    : angle       0.66045 /  0.35 (12283)
  hydrogen bonds       : bond        0.03274 /  2.16 (  404)
  hydrogen bonds       : angle       5.20968 /  3.78 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7535 (m-40) cc_final: 0.6993 (t0)
REVERT: B   56 LYS cc_start: 0.6477 (ptmt) cc_final: 0.6263 (pttt)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0757
  time to fit residues: 15.0503
Evaluate side-chains
  105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 814 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5242 r_free = 0.5242 target = 0.320559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5180 r_free = 0.5180 target = 0.300298 restraints weight = 7014.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.5177 r_free = 0.5177 target = 0.299256 restraints weight = 10307.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.5176 r_free = 0.5176 target = 0.298964 restraints weight = 11102.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.5175 r_free = 0.5175 target = 0.298714 restraints weight = 10352.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.5175 r_free = 0.5175 target = 0.298512 restraints weight = 10450.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.5091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5690
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9097  Z= 0.186
  Angle     :  0.685   7.939  12283  Z= 0.363
  Chirality :  0.048   0.239   1434
  Planarity :  0.004   0.046   1556
  Dihedral  :  5.406  25.687   1183
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.88 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.27), residues: 1100
  helix:  1.35 (0.26), residues: 391
  sheet: -1.86 (0.28), residues: 359
  loop : -1.78 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 567 
 TYR   0.013   0.001   TYR B1192 
 PHE   0.033   0.002   PHE B 721 
 TRP   0.032   0.002   TRP B 259 
 HIS   0.009   0.001   HIS B 530 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.19 ( 9097)
  covalent geometry    : angle       0.68533 /  0.36 (12283)
  hydrogen bonds       : bond        0.03388 /  2.24 (  404)
  hydrogen bonds       : angle       5.38427 /  3.90 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7547 (m-40) cc_final: 0.6976 (t0)
REVERT: B   56 LYS cc_start: 0.6534 (ptmt) cc_final: 0.6304 (pttt)
REVERT: B   77 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6733 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0779
  time to fit residues: 16.1329
Evaluate side-chains
  109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0770
   chunk 76 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 85 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 814 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.324963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5201 r_free = 0.5201 target = 0.304514 restraints weight = 6998.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5199 r_free = 0.5199 target = 0.303833 restraints weight = 11119.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5198 r_free = 0.5198 target = 0.303513 restraints weight = 11097.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.5197 r_free = 0.5197 target = 0.303225 restraints weight = 10139.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5196 r_free = 0.5196 target = 0.303047 restraints weight = 10998.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.5121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5638
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9097  Z= 0.156
  Angle     :  0.643   7.759  12283  Z= 0.338
  Chirality :  0.047   0.241   1434
  Planarity :  0.004   0.047   1556
  Dihedral  :  5.232  21.730   1183
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.09 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.27), residues: 1100
  helix:  1.53 (0.26), residues: 385
  sheet: -1.73 (0.28), residues: 348
  loop : -1.73 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 445 
 TYR   0.017   0.001   TYR B 698 
 PHE   0.038   0.002   PHE A  69 
 TRP   0.033   0.002   TRP B 259 
 HIS   0.012   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 ( 9097)
  covalent geometry    : angle       0.64314 /  0.34 (12283)
  hydrogen bonds       : bond        0.03235 /  2.17 (  404)
  hydrogen bonds       : angle       5.19032 /  3.78 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.3216 (p) cc_final: 0.2988 (p)
REVERT: B   40 ASN cc_start: 0.7486 (m-40) cc_final: 0.6930 (t0)
REVERT: B   56 LYS cc_start: 0.6509 (ptmt) cc_final: 0.6276 (pttt)
REVERT: B   77 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6717 (mm-30)
REVERT: B  334 THR cc_start: 0.6023 (p) cc_final: 0.5820 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0761
  time to fit residues: 15.5374
Evaluate side-chains
  108 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0270
   chunk 74 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0970
   chunk 76 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.3236

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 401 HIS
B 814 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5276 r_free = 0.5276 target = 0.328313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5220 r_free = 0.5220 target = 0.309302 restraints weight = 6901.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5219 r_free = 0.5219 target = 0.308885 restraints weight = 10977.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5217 r_free = 0.5217 target = 0.308466 restraints weight = 10406.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.5216 r_free = 0.5216 target = 0.307961 restraints weight = 9858.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.5215 r_free = 0.5215 target = 0.307654 restraints weight = 11126.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.5222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5564
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9097  Z= 0.128
  Angle     :  0.635   7.571  12283  Z= 0.332
  Chirality :  0.046   0.231   1434
  Planarity :  0.004   0.047   1556
  Dihedral  :  5.047  20.328   1183
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.49 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.27), residues: 1100
  helix:  1.48 (0.26), residues: 386
  sheet: -1.66 (0.28), residues: 353
  loop : -1.54 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1085 
 TYR   0.014   0.001   TYR B 258 
 PHE   0.013   0.002   PHE B 647 
 TRP   0.035   0.002   TRP B 259 
 HIS   0.014   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 9097)
  covalent geometry    : angle       0.63525 /  0.33 (12283)
  hydrogen bonds       : bond        0.02986 /  2.01 (  404)
  hydrogen bonds       : angle       5.07657 /  3.70 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.6697 (tpp) cc_final: 0.6087 (mmt)
REVERT: A   80 THR cc_start: 0.3336 (p) cc_final: 0.3114 (p)
REVERT: B   40 ASN cc_start: 0.7465 (m-40) cc_final: 0.6914 (t0)
REVERT: B   56 LYS cc_start: 0.6443 (ptmt) cc_final: 0.6229 (pttt)
REVERT: B  334 THR cc_start: 0.6050 (p) cc_final: 0.5847 (p)
REVERT: B  392 MET cc_start: 0.6353 (mpp) cc_final: 0.6001 (mpp)
REVERT: B  814 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7930 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0709
  time to fit residues: 13.9075
Evaluate side-chains
  108 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0970
   chunk 42 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0070
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0970
   chunk 55 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.1994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 401 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5289 r_free = 0.5289 target = 0.319358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.314047 restraints weight = 6628.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.313981 restraints weight = 9075.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.313897 restraints weight = 8758.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.313795 restraints weight = 8837.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.313770 restraints weight = 9161.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.5277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5381
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9097  Z= 0.118
  Angle     :  0.625   7.928  12283  Z= 0.327
  Chirality :  0.046   0.175   1434
  Planarity :  0.004   0.049   1556
  Dihedral  :  4.901  19.353   1183
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.27), residues: 1100
  helix:  1.49 (0.26), residues: 385
  sheet: -1.38 (0.29), residues: 341
  loop : -1.60 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1085 
 TYR   0.018   0.001   TYR B 338 
 PHE   0.040   0.002   PHE A  69 
 TRP   0.039   0.003   TRP B 259 
 HIS   0.013   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 9097)
  covalent geometry    : angle       0.62536 /  0.33 (12283)
  hydrogen bonds       : bond        0.03025 /  2.01 (  404)
  hydrogen bonds       : angle       4.93350 /  3.59 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 VAL cc_start: 0.6006 (t) cc_final: 0.5797 (t)
REVERT: B   40 ASN cc_start: 0.7296 (m-40) cc_final: 0.6806 (t0)
REVERT: B   56 LYS cc_start: 0.6270 (ptmt) cc_final: 0.6068 (pttt)
REVERT: B  334 THR cc_start: 0.6000 (p) cc_final: 0.5715 (p)
REVERT: B  343 ASP cc_start: 0.5530 (p0) cc_final: 0.5210 (t0)
REVERT: B  814 HIS cc_start: 0.7857 (t-90) cc_final: 0.7617 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0751
  time to fit residues: 14.7879
Evaluate side-chains
  103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0770
   chunk 46 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0980
   chunk 11 optimal weight:    0.0000
   overall best weight:    0.1942

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 401 HIS
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.321371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.316244 restraints weight = 6665.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.315626 restraints weight = 9045.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.315626 restraints weight = 11103.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.315626 restraints weight = 11103.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.315626 restraints weight = 11103.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.5290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5358
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9097  Z= 0.118
  Angle     :  0.628   8.783  12283  Z= 0.326
  Chirality :  0.046   0.177   1434
  Planarity :  0.004   0.050   1556
  Dihedral  :  4.787  18.359   1183
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.27), residues: 1100
  helix:  1.49 (0.26), residues: 384
  sheet: -1.34 (0.29), residues: 343
  loop : -1.60 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 762 
 TYR   0.023   0.001   TYR B 698 
 PHE   0.013   0.001   PHE A  69 
 TRP   0.040   0.002   TRP B 259 
 HIS   0.012   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 9097)
  covalent geometry    : angle       0.62766 /  0.33 (12283)
  hydrogen bonds       : bond        0.02976 /  1.99 (  404)
  hydrogen bonds       : angle       4.90764 /  3.56 ( 1167)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 ASN cc_start: 0.7149 (m-40) cc_final: 0.6783 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0741
  time to fit residues: 14.1742
Evaluate side-chains
  101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 87 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 401 HIS
** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 927 GLN
** B1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5278 r_free = 0.5278 target = 0.315483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.309445 restraints weight = 6652.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.309263 restraints weight = 9559.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.5259 r_free = 0.5259 target = 0.309103 restraints weight = 9421.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.5259 r_free = 0.5259 target = 0.308959 restraints weight = 9484.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5259 r_free = 0.5259 target = 0.308919 restraints weight = 10012.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.5264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5450
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9097  Z= 0.146
  Angle     :  0.645   7.147  12283  Z= 0.337
  Chirality :  0.047   0.174   1434
  Planarity :  0.004   0.036   1556
  Dihedral  :  4.957  21.825   1183
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.27), residues: 1100
  helix:  1.43 (0.26), residues: 392
  sheet: -1.46 (0.29), residues: 344
  loop : -1.63 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 567 
 TYR   0.017   0.001   TYR B 995 
 PHE   0.014   0.002   PHE A 142 
 TRP   0.042   0.002   TRP B 259 
 HIS   0.011   0.001   HIS B 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9097)
  covalent geometry    : angle       0.64548 /  0.34 (12283)
  hydrogen bonds       : bond        0.03068 /  2.04 (  404)
  hydrogen bonds       : angle       5.05962 /  3.64 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1486.95 seconds
wall clock time: 26 minutes 37.42 seconds (1597.42 seconds total)