Starting phenix.real_space_refine
on Wed Sep 17 15:57:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkb_61550/09_2025/9jkb_61550.cif"
  }
  resolution = 3.93
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6063      2.51       5
     N    1602      2.21       5
     O    1819      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9532
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1343
          Classifications: {'peptide': 175}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 8, 'TRANS': 166}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "A"
      Number of atoms: 6015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 6015
          Classifications: {'peptide': 736}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 722}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1257
          Classifications: {'peptide': 158}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 148}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 144
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "D"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 773
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
  Time building chain proxies: 2.38, per 1000 atoms: 0.25
  Number of scatterers: 9532
  At special positions: 0
  Unit cell: (82, 115.62, 181.22, 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      48     16.00
     O    1819      8.00
     N    1602      7.00
     C    6063      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: 0.89
  Conformation dependent library (CDL) restraints added in 364.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      64.0% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'C' and resid 184 through 189
    Processing helix  chain 'C' and resid 192 through 198
      removed outlier: 3.941A  pdb=" N   SER C 196 " --> pdb=" O   SER C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 228
    Processing helix  chain 'C' and resid 276 through 281
      removed outlier: 3.968A  pdb=" N   LYS C 281 " --> pdb=" O   PRO C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 314
    Processing helix  chain 'C' and resid 315 through 319
      removed outlier: 3.681A  pdb=" N   GLY C 319 " --> pdb=" O   PRO C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 348
    Processing helix  chain 'C' and resid 349 through 354
      removed outlier: 3.843A  pdb=" N   LEU C 352 " --> pdb=" O   HIS C 349 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN C 354 " --> pdb=" O   ASN C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 369 through 380
      removed outlier: 3.620A  pdb=" N   ILE C 377 " --> pdb=" O   GLY C 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 33
      removed outlier: 4.348A  pdb=" N   ASP A  22 " --> pdb=" O   ASP A  18 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ASP A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 54
    Processing helix  chain 'A' and resid 85 through 107
      removed outlier: 3.574A  pdb=" N   ARG A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP A 106 " --> pdb=" O   ASN A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 137
      removed outlier: 3.670A  pdb=" N   LEU A 116 " --> pdb=" O   ASP A 112 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LYS A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 152
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.543A  pdb=" N   LEU A 171 " --> pdb=" O   TRP A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.820A  pdb=" N   LYS A 177 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   GLN A 178 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 4.276A  pdb=" N   ILE A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
    Processing helix  chain 'A' and resid 232 through 255
    Processing helix  chain 'A' and resid 256 through 279
      removed outlier: 3.583A  pdb=" N   LEU A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 4.310A  pdb=" N   GLU A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 313
      removed outlier: 3.781A  pdb=" N   GLN A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ASN A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 327
    Processing helix  chain 'A' and resid 332 through 356
      removed outlier: 4.439A  pdb=" N   LEU A 336 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
    Processing helix  chain 'A' and resid 362 through 384
      removed outlier: 3.774A  pdb=" N   TYR A 366 " --> pdb=" O   ASP A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 405
      removed outlier: 3.783A  pdb=" N   ASN A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 412
    Processing helix  chain 'A' and resid 416 through 429
      removed outlier: 3.526A  pdb=" N   GLU A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 454
    Processing helix  chain 'A' and resid 458 through 476
      removed outlier: 3.579A  pdb=" N   PHE A 462 " --> pdb=" O   ASP A 458 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   HIS A 476 " --> pdb=" O   LYS A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 497
      removed outlier: 3.503A  pdb=" N   GLU A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 528
    Processing helix  chain 'A' and resid 556 through 574
      removed outlier: 3.634A  pdb=" N   SER A 562 " --> pdb=" O   GLU A 558 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG A 565 " --> pdb=" O   ARG A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 617
    Processing helix  chain 'A' and resid 622 through 630
    Processing helix  chain 'A' and resid 632 through 647
    Processing helix  chain 'A' and resid 688 through 723
      removed outlier: 3.533A  pdb=" N   LYS A 720 " --> pdb=" O   VAL A 716 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   MET A 721 " --> pdb=" O   ARG A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 739
    Processing helix  chain 'A' and resid 745 through 758
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 24 through 33
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 86 through 93
    Processing helix  chain 'B' and resid 96 through 110
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 131 through 140
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 3.813A  pdb=" N   ARG B 154 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 73
      removed outlier: 3.743A  pdb=" N   PHE D  73 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 84
      removed outlier: 3.556A  pdb=" N   CYS D  80 " --> pdb=" O   PRO D  76 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLN D  81 " --> pdb=" O   HIS D  77 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU D  82 " --> pdb=" O   ASP D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 92
      removed outlier: 4.256A  pdb=" N   GLU D  91 " --> pdb=" O   HIS D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 107
    Processing helix  chain 'D' and resid 121 through 125
    Processing helix  chain 'D' and resid 138 through 147
    Processing sheet with id=AA1, first strand: chain 'C' and resid 234 through 235
      removed outlier: 3.574A  pdb=" N   SER C 329 " --> pdb=" O   GLN C 360 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE C 331 " --> pdb=" O   THR C 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 541
      removed outlier: 6.623A  pdb=" N   GLN A 538 " --> pdb=" O   ALA R  31 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   TRP R  33 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU A 540 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   TRP R  35 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 589
      removed outlier: 3.557A  pdb=" N   GLY A 588 " --> pdb=" O   ALA A 603 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA A 603 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 621
      removed outlier: 3.513A  pdb=" N   VAL A 650 " --> pdb=" O   LYS A 670 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 763 through 764
    Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 4

    529 hydrogen bonds defined for protein.
    1554 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: 1.69

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3127
        1.34 -     1.46: 1914
        1.46 -     1.58: 4600
        1.58 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 9716
  Sorted by residual:
  bond pdb=" C   LYS D 126 "
       pdb=" N   PRO D 127 "
    ideal  model  delta    sigma   weight residual
    1.337  1.376 -0.040 1.11e-02 8.12e+03 1.29e+01
  bond pdb=" N   ASN D  86 "
       pdb=" CA  ASN D  86 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.020 1.29e-02 6.01e+03 2.45e+00
  bond pdb=" C   VAL A 746 "
       pdb=" N   PRO A 747 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 1.36e-02 5.41e+03 1.15e+00
  bond pdb=" N   ASN B 140 "
       pdb=" CA  ASN B 140 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.42e-02 4.96e+03 9.56e-01
  bond pdb=" CA  LYS D 126 "
       pdb=" C   LYS D 126 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.26e-02 6.30e+03 9.21e-01
  ... (remaining 9711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 13016
        2.85 -     5.70: 99
        5.70 -     8.56: 13
        8.56 -    11.41: 2
       11.41 -    14.26: 2
  Bond angle restraints: 13132
  Sorted by residual:
  angle pdb=" CA  LEU C 367 "
        pdb=" CB  LEU C 367 "
        pdb=" CG  LEU C 367 "
      ideal   model   delta    sigma   weight residual
     116.30  130.56  -14.26 3.50e+00 8.16e-02 1.66e+01
  angle pdb=" C   ARG A 401 "
        pdb=" N   PHE A 402 "
        pdb=" CA  PHE A 402 "
      ideal   model   delta    sigma   weight residual
     122.54  116.16    6.38 1.65e+00 3.67e-01 1.49e+01
  angle pdb=" CA  LEU D 121 "
        pdb=" CB  LEU D 121 "
        pdb=" CG  LEU D 121 "
      ideal   model   delta    sigma   weight residual
     116.30  129.46  -13.16 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" C   GLN B  90 "
        pdb=" N   GLU B  91 "
        pdb=" CA  GLU B  91 "
      ideal   model   delta    sigma   weight residual
     121.58  114.46    7.12 1.95e+00 2.63e-01 1.33e+01
  angle pdb=" CA  TYR A 570 "
        pdb=" CB  TYR A 570 "
        pdb=" CG  TYR A 570 "
      ideal   model   delta    sigma   weight residual
     113.90  120.16   -6.26 1.80e+00 3.09e-01 1.21e+01
  ... (remaining 13127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 5165
       17.66 -    35.32: 601
       35.32 -    52.98: 114
       52.98 -    70.64: 21
       70.64 -    88.30: 13
  Dihedral angle restraints: 5914
    sinusoidal: 2431
      harmonic: 3483
  Sorted by residual:
  dihedral pdb=" CA  ILE A  20 "
           pdb=" C   ILE A  20 "
           pdb=" N   TRP A  21 "
           pdb=" CA  TRP A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.75  -21.25     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  GLU A 758 "
           pdb=" C   GLU A 758 "
           pdb=" N   LYS A 759 "
           pdb=" CA  LYS A 759 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  CYS A 137 "
           pdb=" C   CYS A 137 "
           pdb=" N   ALA A 138 "
           pdb=" CA  ALA A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 959
       0.035 -    0.071: 349
       0.071 -    0.106: 113
       0.106 -    0.142: 40
       0.142 -    0.177: 5
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CB  VAL B  95 "
            pdb=" CA  VAL B  95 "
            pdb=" CG1 VAL B  95 "
            pdb=" CG2 VAL B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CA  GLU A 758 "
            pdb=" N   GLU A 758 "
            pdb=" C   GLU A 758 "
            pdb=" CB  GLU A 758 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CB  VAL B  25 "
            pdb=" CA  VAL B  25 "
            pdb=" CG1 VAL B  25 "
            pdb=" CG2 VAL B  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1463 not shown)

  Planarity restraints: 1685
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 136 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.19e+00
        pdb=" C   ILE A 136 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ILE A 136 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   CYS A 137 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 124 "    0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" C   GLU A 124 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLU A 124 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 125 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 119 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.94e+00
        pdb=" C   TYR A 119 "    0.042 2.00e-02 2.50e+03
        pdb=" O   TYR A 119 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR A 120 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1682 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2176
        2.78 -     3.31: 9744
        3.31 -     3.84: 16636
        3.84 -     4.37: 18090
        4.37 -     4.90: 30594
  Nonbonded interactions: 77240
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 260 "
            pdb=" O   LEU A 295 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   GLY A 212 "
            pdb=" OG1 THR A 224 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ILE C 310 "
            pdb=" OG1 THR C 314 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   CYS D  80 "
            pdb=" OG  SER D  84 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER A 514 "
            pdb=" O   VAL A 539 "
     model   vdw
     2.297 3.040
  ... (remaining 77235 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:             12.990
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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   0.040   9716  Z= 0.156
  Angle     :  0.672  14.258  13132  Z= 0.341
  Chirality :  0.043   0.177   1466
  Planarity :  0.005   0.060   1685
  Dihedral  : 15.640  88.304   3648
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.62 %
  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 aren not related in a simple way.
  whole: -0.64 (0.23), residues: 1165
  helix:  0.16 (0.19), residues: 693
  sheet: -1.96 (0.87), residues: 33
  loop : -1.11 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 707 
 TYR   0.035   0.001   TYR A 570 
 PHE   0.025   0.001   PHE A 402 
 TRP   0.009   0.001   TRP A 167 
 HIS   0.008   0.001   HIS C 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9716)
  covalent geometry    : angle       0.67207 (13132)
  hydrogen bonds       : bond        0.17507 (  529)
  hydrogen bonds       : angle       6.43084 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 243
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 GLN cc_start: 0.8751 (tt0) cc_final: 0.8315 (tt0)
REVERT: C  315 ASP cc_start: 0.5268 (m-30) cc_final: 0.4996 (m-30)
REVERT: C  342 PHE cc_start: 0.8383 (m-80) cc_final: 0.8137 (m-10)
REVERT: C  351 ASN cc_start: 0.8171 (p0) cc_final: 0.7504 (t0)
REVERT: A  341 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: A  411 MET cc_start: 0.7919 (mtp) cc_final: 0.7653 (mtm)
REVERT: A  566 PHE cc_start: 0.8645 (t80) cc_final: 0.8074 (t80)
REVERT: A  632 LYS cc_start: 0.9272 (ptpt) cc_final: 0.9037 (ptpt)
REVERT: A  640 LEU cc_start: 0.9081 (mp) cc_final: 0.8841 (pp)
REVERT: A  664 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8663 (mppt)
REVERT: A  701 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8869 (tptt)
REVERT: B   31 LEU cc_start: 0.8989 (mm) cc_final: 0.8459 (tp)
REVERT: B   60 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: R   25 LYS cc_start: 0.8187 (pttm) cc_final: 0.7875 (pttm)
REVERT: D   57 SER cc_start: 0.6427 (t) cc_final: 0.6051 (m)
REVERT: D   69 TYR cc_start: 0.8907 (t80) cc_final: 0.8566 (t80)
REVERT: D  105 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8156 (ttp-170)
REVERT: D  115 TRP cc_start: 0.8396 (p-90) cc_final: 0.8153 (p-90)
  outliers start: 2
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1200
  time to fit residues: 39.5549
Evaluate side-chains
  161 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0040
   chunk 113 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 ASN
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.132493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.094992 restraints weight = 25043.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.095472 restraints weight = 12865.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.096776 restraints weight = 9720.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.096682 restraints weight = 8129.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.097006 restraints weight = 8085.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9716  Z= 0.147
  Angle     :  0.636  11.566  13132  Z= 0.326
  Chirality :  0.042   0.169   1466
  Planarity :  0.004   0.059   1685
  Dihedral  :  4.154  22.227   1267
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  9.88 %
    Favored  : 88.03 %
  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 aren not related in a simple way.
  whole:  0.03 (0.24), residues: 1165
  helix:  0.88 (0.19), residues: 701
  sheet: -1.95 (0.83), residues: 33
  loop : -1.19 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 707 
 TYR   0.029   0.002   TYR A 570 
 PHE   0.023   0.002   PHE A 402 
 TRP   0.024   0.002   TRP C 303 
 HIS   0.011   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9716)
  covalent geometry    : angle       0.63641 (13132)
  hydrogen bonds       : bond        0.04543 (  529)
  hydrogen bonds       : angle       4.80832 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  315 ASP cc_start: 0.5391 (m-30) cc_final: 0.5085 (m-30)
REVERT: C  370 PHE cc_start: 0.7607 (m-10) cc_final: 0.7296 (m-10)
REVERT: A  199 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.8259 (tpp-160)
REVERT: A  409 THR cc_start: 0.8642 (p) cc_final: 0.8340 (t)
REVERT: A  566 PHE cc_start: 0.8575 (t80) cc_final: 0.8180 (t80)
REVERT: A  632 LYS cc_start: 0.9356 (ptpt) cc_final: 0.9138 (ptpp)
REVERT: A  664 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8694 (mppt)
REVERT: A  701 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8856 (tptt)
REVERT: A  719 MET cc_start: 0.4294 (tpp) cc_final: 0.4070 (tpp)
REVERT: B   14 PHE cc_start: 0.7764 (m-80) cc_final: 0.7535 (m-80)
REVERT: B   60 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: B  100 LEU cc_start: 0.8290 (tt) cc_final: 0.7865 (tp)
REVERT: B  157 ASN cc_start: 0.8651 (p0) cc_final: 0.8385 (p0)
REVERT: D   57 SER cc_start: 0.6615 (t) cc_final: 0.6301 (p)
REVERT: D   61 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7764 (mmm-85)
REVERT: D  133 ASP cc_start: 0.7532 (p0) cc_final: 0.6964 (t0)
  outliers start: 22
  outliers final: 12
  residues processed: 196
  average time/residue: 0.1053
  time to fit residues: 28.9388
Evaluate side-chains
  162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  253 GLN
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 333 GLN
C 351 ASN
A 253 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 ASN
B  65 HIS
B 158 GLN
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.131320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.094216 restraints weight = 24849.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.094291 restraints weight = 12551.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.095396 restraints weight = 9844.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095429 restraints weight = 8471.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.095537 restraints weight = 7996.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9716  Z= 0.148
  Angle     :  0.614  11.504  13132  Z= 0.316
  Chirality :  0.041   0.184   1466
  Planarity :  0.004   0.057   1685
  Dihedral  :  4.035  22.604   1267
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.68 %
    Favored  : 84.05 %
  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 aren not related in a simple way.
  whole:  0.26 (0.24), residues: 1165
  helix:  1.11 (0.19), residues: 692
  sheet: -2.71 (0.85), residues: 30
  loop : -1.09 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 100 
 TYR   0.024   0.002   TYR A 570 
 PHE   0.026   0.002   PHE C 342 
 TRP   0.016   0.001   TRP C 303 
 HIS   0.017   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9716)
  covalent geometry    : angle       0.61419 (13132)
  hydrogen bonds       : bond        0.04084 (  529)
  hydrogen bonds       : angle       4.58587 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 PHE cc_start: 0.3215 (OUTLIER) cc_final: 0.2640 (m-80)
REVERT: C  315 ASP cc_start: 0.5354 (m-30) cc_final: 0.5011 (m-30)
REVERT: C  351 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7850 (p0)
REVERT: A  261 MET cc_start: 0.8866 (mtp) cc_final: 0.8459 (ttt)
REVERT: A  409 THR cc_start: 0.8623 (p) cc_final: 0.8281 (t)
REVERT: A  632 LYS cc_start: 0.9379 (ptpt) cc_final: 0.9124 (ptpp)
REVERT: A  640 LEU cc_start: 0.9197 (mt) cc_final: 0.8597 (pp)
REVERT: A  664 LYS cc_start: 0.9244 (mmtm) cc_final: 0.8731 (mppt)
REVERT: A  701 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8870 (tptt)
REVERT: A  719 MET cc_start: 0.4738 (tpp) cc_final: 0.4503 (tpp)
REVERT: B   60 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: B  157 ASN cc_start: 0.8654 (p0) cc_final: 0.8425 (p0)
REVERT: D   57 SER cc_start: 0.6713 (t) cc_final: 0.6410 (m)
REVERT: D   61 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7851 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8648 (p-90) cc_final: 0.8183 (p-90)
REVERT: D  133 ASP cc_start: 0.7475 (p0) cc_final: 0.6827 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 173
  average time/residue: 0.0965
  time to fit residues: 24.1115
Evaluate side-chains
  162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain C residue  351 ASN
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  253 GLN
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain R residue   25 LYS
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 ASN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 ASN
B  49 ASN
B 158 GLN
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.130531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.092816 restraints weight = 25046.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.093012 restraints weight = 12704.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.093997 restraints weight = 9912.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094095 restraints weight = 8475.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.094179 restraints weight = 8115.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9716  Z= 0.170
  Angle     :  0.625  10.702  13132  Z= 0.321
  Chirality :  0.042   0.230   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.034  21.776   1267
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.10 %
    Favored  : 82.15 %
  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 aren not related in a simple way.
  whole:  0.30 (0.24), residues: 1165
  helix:  1.14 (0.19), residues: 692
  sheet: -2.04 (0.77), residues: 33
  loop : -1.12 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 745 
 TYR   0.030   0.002   TYR A 570 
 PHE   0.024   0.002   PHE C 342 
 TRP   0.018   0.001   TRP C 303 
 HIS   0.012   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9716)
  covalent geometry    : angle       0.62547 (13132)
  hydrogen bonds       : bond        0.03979 (  529)
  hydrogen bonds       : angle       4.55102 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 PHE cc_start: 0.3117 (OUTLIER) cc_final: 0.2666 (m-80)
REVERT: C  315 ASP cc_start: 0.5296 (m-30) cc_final: 0.4899 (m-30)
REVERT: C  351 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7726 (p0)
REVERT: C  370 PHE cc_start: 0.7692 (m-10) cc_final: 0.7436 (m-10)
REVERT: A   37 MET cc_start: 0.9048 (ppp) cc_final: 0.8812 (ppp)
REVERT: A  199 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8227 (tpp-160)
REVERT: A  261 MET cc_start: 0.8879 (mtp) cc_final: 0.8383 (ttt)
REVERT: A  305 THR cc_start: 0.9162 (m) cc_final: 0.8704 (p)
REVERT: A  409 THR cc_start: 0.8657 (p) cc_final: 0.8321 (t)
REVERT: A  570 TYR cc_start: 0.7490 (p90) cc_final: 0.7099 (p90)
REVERT: A  640 LEU cc_start: 0.9234 (mt) cc_final: 0.8755 (pp)
REVERT: A  664 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8730 (mppt)
REVERT: A  701 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8885 (tptt)
REVERT: A  719 MET cc_start: 0.4681 (tpp) cc_final: 0.4334 (tpp)
REVERT: B   60 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: B  157 ASN cc_start: 0.8673 (p0) cc_final: 0.8425 (p0)
REVERT: D   57 SER cc_start: 0.6571 (t) cc_final: 0.6358 (m)
REVERT: D   61 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7845 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8704 (p-90) cc_final: 0.8241 (p-90)
REVERT: D  133 ASP cc_start: 0.7524 (p0) cc_final: 0.6847 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 174
  average time/residue: 0.0958
  time to fit residues: 24.1714
Evaluate side-chains
  166 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  351 ASN
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  672 TYR
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 54 optimal weight:    0.0070
   chunk 56 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0270
   chunk 93 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.4062

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

Flipped N/Q/H residues before XYZ refinement:
** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 ASN
A 343 HIS
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3919 r_free = 0.3919 target = 0.120605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084987 restraints weight = 24152.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083409 restraints weight = 15064.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.083980 restraints weight = 13508.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.084124 restraints weight = 11611.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.084204 restraints weight = 10644.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   9716  Z= 0.247
  Angle     :  0.678   9.752  13132  Z= 0.350
  Chirality :  0.044   0.176   1466
  Planarity :  0.004   0.057   1685
  Dihedral  :  4.161  24.225   1267
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.66 %
    Favored  : 78.73 %
  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 aren not related in a simple way.
  whole:  0.16 (0.24), residues: 1165
  helix:  1.01 (0.19), residues: 692
  sheet: -1.92 (0.79), residues: 33
  loop : -1.15 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 565 
 TYR   0.026   0.002   TYR A 278 
 PHE   0.019   0.002   PHE A 402 
 TRP   0.021   0.002   TRP C 303 
 HIS   0.010   0.002   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 9716)
  covalent geometry    : angle       0.67759 (13132)
  hydrogen bonds       : bond        0.04252 (  529)
  hydrogen bonds       : angle       4.67982 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6781 (p90) cc_final: 0.6169 (p90)
REVERT: C  289 PHE cc_start: 0.3549 (OUTLIER) cc_final: 0.3037 (m-80)
REVERT: C  315 ASP cc_start: 0.5379 (m-30) cc_final: 0.4983 (m-30)
REVERT: C  342 PHE cc_start: 0.8761 (m-10) cc_final: 0.8449 (m-10)
REVERT: C  357 TRP cc_start: 0.8067 (p-90) cc_final: 0.7569 (p-90)
REVERT: A   37 MET cc_start: 0.9077 (ppp) cc_final: 0.8852 (ppp)
REVERT: A  331 ASP cc_start: 0.7995 (t0) cc_final: 0.7714 (t0)
REVERT: A  508 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7977 (m-80)
REVERT: A  570 TYR cc_start: 0.7608 (p90) cc_final: 0.7080 (p90)
REVERT: A  664 LYS cc_start: 0.9282 (mmtm) cc_final: 0.8959 (mppt)
REVERT: A  701 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8888 (tptt)
REVERT: A  719 MET cc_start: 0.4680 (tpp) cc_final: 0.4454 (tpp)
REVERT: B   14 PHE cc_start: 0.7830 (m-80) cc_final: 0.7568 (m-80)
REVERT: B   60 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: B  157 ASN cc_start: 0.8659 (p0) cc_final: 0.8395 (p0)
REVERT: D   61 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7814 (mtp85)
REVERT: D  133 ASP cc_start: 0.7436 (p0) cc_final: 0.6750 (t0)
REVERT: D  145 MET cc_start: 0.7849 (tmm) cc_final: 0.7647 (tmm)
  outliers start: 38
  outliers final: 24
  residues processed: 170
  average time/residue: 0.0933
  time to fit residues: 23.3012
Evaluate side-chains
  158 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  672 TYR
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 104 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 67 optimal weight:    0.4980
   chunk 111 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0070
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
C 229 HIS
** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 ASN
A  35 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.123350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.087784 restraints weight = 23947.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.086137 restraints weight = 14632.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.086778 restraints weight = 12942.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086889 restraints weight = 11409.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.087095 restraints weight = 10538.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9716  Z= 0.137
  Angle     :  0.616   9.737  13132  Z= 0.313
  Chirality :  0.041   0.172   1466
  Planarity :  0.004   0.057   1685
  Dihedral  :  4.055  22.724   1267
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.56 %
    Favored  : 77.59 %
  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 aren not related in a simple way.
  whole:  0.31 (0.24), residues: 1165
  helix:  1.13 (0.19), residues: 694
  sheet: -1.94 (0.76), residues: 33
  loop : -1.08 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 745 
 TYR   0.020   0.002   TYR A 570 
 PHE   0.026   0.002   PHE A 498 
 TRP   0.025   0.001   TRP C 303 
 HIS   0.012   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9716)
  covalent geometry    : angle       0.61593 (13132)
  hydrogen bonds       : bond        0.03895 (  529)
  hydrogen bonds       : angle       4.49012 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6535 (p90) cc_final: 0.6052 (p90)
REVERT: C  289 PHE cc_start: 0.2993 (OUTLIER) cc_final: 0.2516 (m-80)
REVERT: C  315 ASP cc_start: 0.5321 (m-30) cc_final: 0.4973 (m-30)
REVERT: C  370 PHE cc_start: 0.7767 (m-10) cc_final: 0.7515 (m-10)
REVERT: A  331 ASP cc_start: 0.7921 (t0) cc_final: 0.7653 (t0)
REVERT: A  570 TYR cc_start: 0.7566 (p90) cc_final: 0.7054 (p90)
REVERT: A  633 MET cc_start: 0.8709 (tpt) cc_final: 0.7976 (pmm)
REVERT: A  664 LYS cc_start: 0.9268 (mmtm) cc_final: 0.8945 (mppt)
REVERT: A  701 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8851 (tptt)
REVERT: B   60 GLN cc_start: 0.8304 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: B  126 MET cc_start: 0.8462 (tmm) cc_final: 0.7968 (mtt)
REVERT: B  157 ASN cc_start: 0.8582 (p0) cc_final: 0.8275 (p0)
REVERT: D   61 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7641 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8555 (p-90) cc_final: 0.8073 (p-90)
REVERT: D  133 ASP cc_start: 0.7408 (p0) cc_final: 0.6732 (t0)
  outliers start: 30
  outliers final: 20
  residues processed: 170
  average time/residue: 0.1007
  time to fit residues: 24.4848
Evaluate side-chains
  152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  672 TYR
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0070
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.3602

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

Flipped N/Q/H residues before XYZ refinement:
C 351 ASN
A 280 HIS
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3912 r_free = 0.3912 target = 0.120146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.083538 restraints weight = 24336.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.082554 restraints weight = 16330.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.083357 restraints weight = 13591.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.083138 restraints weight = 12531.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.083388 restraints weight = 11538.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   9716  Z= 0.243
  Angle     :  0.709  14.566  13132  Z= 0.362
  Chirality :  0.044   0.175   1466
  Planarity :  0.004   0.057   1685
  Dihedral  :  4.201  23.175   1267
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.56 %
    Favored  : 76.73 %
  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 aren not related in a simple way.
  whole:  0.15 (0.24), residues: 1165
  helix:  0.98 (0.19), residues: 694
  sheet: -2.33 (0.67), residues: 38
  loop : -1.07 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 565 
 TYR   0.029   0.002   TYR A 278 
 PHE   0.026   0.002   PHE A 498 
 TRP   0.029   0.002   TRP C 303 
 HIS   0.013   0.002   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 9716)
  covalent geometry    : angle       0.70850 (13132)
  hydrogen bonds       : bond        0.04335 (  529)
  hydrogen bonds       : angle       4.72359 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6653 (p90) cc_final: 0.6190 (p90)
REVERT: C  289 PHE cc_start: 0.3662 (OUTLIER) cc_final: 0.3044 (m-80)
REVERT: C  315 ASP cc_start: 0.5171 (m-30) cc_final: 0.4843 (m-30)
REVERT: A  331 ASP cc_start: 0.8089 (t0) cc_final: 0.7778 (t0)
REVERT: A  570 TYR cc_start: 0.7818 (p90) cc_final: 0.7252 (p90)
REVERT: A  608 MET cc_start: 0.8624 (mpp) cc_final: 0.8361 (mpp)
REVERT: A  664 LYS cc_start: 0.9311 (mmtm) cc_final: 0.8984 (mppt)
REVERT: A  701 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8887 (tptt)
REVERT: B   14 PHE cc_start: 0.7860 (m-80) cc_final: 0.7591 (m-80)
REVERT: B   60 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: B  157 ASN cc_start: 0.8675 (p0) cc_final: 0.8443 (p0)
REVERT: D   61 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7803 (mtp85)
REVERT: D  115 TRP cc_start: 0.8634 (p-90) cc_final: 0.8396 (p-90)
REVERT: D  133 ASP cc_start: 0.7522 (p0) cc_final: 0.6838 (t0)
REVERT: D  145 MET cc_start: 0.8024 (tmm) cc_final: 0.7584 (tmm)
  outliers start: 39
  outliers final: 30
  residues processed: 159
  average time/residue: 0.0989
  time to fit residues: 22.6011
Evaluate side-chains
  159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain C residue  351 ASN
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  672 TYR
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  147 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   chunk 9 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
C 229 HIS
C 351 ASN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.122752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.093436 restraints weight = 24377.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.093064 restraints weight = 27184.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.093725 restraints weight = 24392.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.095379 restraints weight = 14973.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.095486 restraints weight = 12060.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   9716  Z= 0.140
  Angle     :  0.664   9.108  13132  Z= 0.336
  Chirality :  0.042   0.178   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.148  23.863   1267
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.08 %
    Favored  : 76.07 %
  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 aren not related in a simple way.
  whole:  0.26 (0.24), residues: 1165
  helix:  1.03 (0.20), residues: 695
  sheet: -2.90 (0.77), residues: 27
  loop : -0.95 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 745 
 TYR   0.023   0.002   TYR A 278 
 PHE   0.031   0.002   PHE A 498 
 TRP   0.033   0.002   TRP C 303 
 HIS   0.015   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9716)
  covalent geometry    : angle       0.66448 (13132)
  hydrogen bonds       : bond        0.03999 (  529)
  hydrogen bonds       : angle       4.61127 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.5802 (p90) cc_final: 0.5437 (p90)
REVERT: C  289 PHE cc_start: 0.2944 (OUTLIER) cc_final: 0.2466 (m-80)
REVERT: C  315 ASP cc_start: 0.5245 (m-30) cc_final: 0.4903 (m-30)
REVERT: A  322 MET cc_start: 0.8727 (tpt) cc_final: 0.8376 (tpt)
REVERT: A  331 ASP cc_start: 0.7953 (t0) cc_final: 0.7663 (t0)
REVERT: A  409 THR cc_start: 0.8591 (p) cc_final: 0.8376 (t)
REVERT: A  450 MET cc_start: 0.8782 (tpp) cc_final: 0.8440 (tpp)
REVERT: A  633 MET cc_start: 0.8175 (tpt) cc_final: 0.7791 (pmm)
REVERT: A  664 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8834 (mppt)
REVERT: B   60 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: B  157 ASN cc_start: 0.8373 (p0) cc_final: 0.8159 (p0)
REVERT: D   61 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7822 (mmm-85)
REVERT: D  133 ASP cc_start: 0.7078 (p0) cc_final: 0.6523 (t0)
REVERT: D  145 MET cc_start: 0.7919 (tmm) cc_final: 0.7440 (tmm)
  outliers start: 30
  outliers final: 21
  residues processed: 171
  average time/residue: 0.1086
  time to fit residues: 26.1822
Evaluate side-chains
  154 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  672 TYR
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 111 optimal weight:    0.0060
   chunk 106 optimal weight:    0.0030
   chunk 109 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.4806

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

Flipped N/Q/H residues before XYZ refinement:
** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.122765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.086789 restraints weight = 24547.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.085186 restraints weight = 14824.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.085759 restraints weight = 13272.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.085910 restraints weight = 11962.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.085965 restraints weight = 10973.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9716  Z= 0.143
  Angle     :  0.689  10.112  13132  Z= 0.347
  Chirality :  0.043   0.239   1466
  Planarity :  0.004   0.062   1685
  Dihedral  :  4.158  23.231   1267
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.46 %
    Favored  : 75.88 %
  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 aren not related in a simple way.
  whole:  0.18 (0.24), residues: 1165
  helix:  0.93 (0.19), residues: 701
  sheet: -2.84 (0.78), residues: 27
  loop : -0.94 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 745 
 TYR   0.022   0.002   TYR A 278 
 PHE   0.031   0.002   PHE A 498 
 TRP   0.033   0.002   TRP C 303 
 HIS   0.014   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9716)
  covalent geometry    : angle       0.68894 (13132)
  hydrogen bonds       : bond        0.04012 (  529)
  hydrogen bonds       : angle       4.66107 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6417 (p90) cc_final: 0.5998 (p90)
REVERT: C  289 PHE cc_start: 0.3321 (OUTLIER) cc_final: 0.2814 (m-80)
REVERT: C  315 ASP cc_start: 0.5267 (m-30) cc_final: 0.4911 (m-30)
REVERT: A  261 MET cc_start: 0.8288 (ttt) cc_final: 0.7827 (ttt)
REVERT: A  305 THR cc_start: 0.9185 (m) cc_final: 0.8728 (p)
REVERT: A  322 MET cc_start: 0.8805 (tpt) cc_final: 0.8519 (tpt)
REVERT: A  331 ASP cc_start: 0.7951 (t0) cc_final: 0.7685 (t0)
REVERT: A  409 THR cc_start: 0.8624 (p) cc_final: 0.8407 (t)
REVERT: A  570 TYR cc_start: 0.7253 (p90) cc_final: 0.6991 (p90)
REVERT: A  633 MET cc_start: 0.8897 (tpt) cc_final: 0.8096 (pmm)
REVERT: A  664 LYS cc_start: 0.9302 (mmtm) cc_final: 0.8745 (mppt)
REVERT: B   60 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8047 (tm-30)
REVERT: D   61 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7965 (mmm-85)
REVERT: D  133 ASP cc_start: 0.7580 (p0) cc_final: 0.6842 (t0)
REVERT: D  145 MET cc_start: 0.8001 (tmm) cc_final: 0.7503 (tmm)
  outliers start: 28
  outliers final: 21
  residues processed: 157
  average time/residue: 0.0980
  time to fit residues: 22.2932
Evaluate side-chains
  155 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain C residue  377 ILE
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    0.0040
   chunk 13 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 3 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 81 optimal weight:    0.3980
   chunk 5 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
C 229 HIS
** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3956 r_free = 0.3956 target = 0.123029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.087523 restraints weight = 24435.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.085573 restraints weight = 15355.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.086332 restraints weight = 13583.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.086474 restraints weight = 11827.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.086793 restraints weight = 10771.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9716  Z= 0.142
  Angle     :  0.694  10.131  13132  Z= 0.350
  Chirality :  0.043   0.231   1466
  Planarity :  0.004   0.065   1685
  Dihedral  :  4.119  22.747   1267
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.51 %
    Favored  : 74.93 %
  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 aren not related in a simple way.
  whole:  0.18 (0.24), residues: 1165
  helix:  0.88 (0.19), residues: 708
  sheet: -2.73 (0.79), residues: 27
  loop : -0.90 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 745 
 TYR   0.027   0.002   TYR D 101 
 PHE   0.031   0.002   PHE A 498 
 TRP   0.037   0.002   TRP C 303 
 HIS   0.015   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9716)
  covalent geometry    : angle       0.69443 (13132)
  hydrogen bonds       : bond        0.03994 (  529)
  hydrogen bonds       : angle       4.64417 ( 1554)

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

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

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2330 Ramachandran restraints generated.
    1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6408 (p90) cc_final: 0.5918 (p90)
REVERT: C  289 PHE cc_start: 0.3106 (OUTLIER) cc_final: 0.2573 (m-80)
REVERT: C  315 ASP cc_start: 0.5315 (m-30) cc_final: 0.4964 (m-30)
REVERT: A  261 MET cc_start: 0.8017 (ttt) cc_final: 0.7522 (ttt)
REVERT: A  305 THR cc_start: 0.9188 (m) cc_final: 0.8698 (p)
REVERT: A  322 MET cc_start: 0.8995 (tpt) cc_final: 0.8456 (tpt)
REVERT: A  331 ASP cc_start: 0.7975 (t0) cc_final: 0.7718 (t0)
REVERT: A  409 THR cc_start: 0.8649 (p) cc_final: 0.8443 (t)
REVERT: A  450 MET cc_start: 0.8736 (tpp) cc_final: 0.8436 (tpp)
REVERT: A  570 TYR cc_start: 0.7397 (p90) cc_final: 0.7079 (p90)
REVERT: A  633 MET cc_start: 0.8907 (tpt) cc_final: 0.8088 (pmm)
REVERT: A  664 LYS cc_start: 0.9293 (mmtm) cc_final: 0.8737 (mppt)
REVERT: B   60 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8073 (tm-30)
REVERT: D   61 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7554 (mtm110)
REVERT: D  107 LEU cc_start: 0.8714 (tp) cc_final: 0.8326 (tp)
REVERT: D  133 ASP cc_start: 0.7579 (p0) cc_final: 0.6842 (t0)
REVERT: D  145 MET cc_start: 0.8018 (tmm) cc_final: 0.7511 (tmm)
  outliers start: 27
  outliers final: 24
  residues processed: 155
  average time/residue: 0.0930
  time to fit residues: 21.3467
Evaluate side-chains
  152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  289 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain C residue  377 ILE
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain R residue   24 VAL
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** D  87 HIS ** 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 = 0.3950 r_free = 0.3950 target = 0.122561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.092477 restraints weight = 24337.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.091426 restraints weight = 24501.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.092091 restraints weight = 24410.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.092502 restraints weight = 15617.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.092788 restraints weight = 13455.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9716  Z= 0.156
  Angle     :  0.697  11.206  13132  Z= 0.351
  Chirality :  0.043   0.238   1466
  Planarity :  0.004   0.065   1685
  Dihedral  :  4.150  22.725   1267
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.70 %
    Favored  : 74.64 %
  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 aren not related in a simple way.
  whole:  0.20 (0.24), residues: 1165
  helix:  0.89 (0.19), residues: 709
  sheet: -2.62 (0.78), residues: 27
  loop : -0.88 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 565 
 TYR   0.021   0.002   TYR A 278 
 PHE   0.021   0.002   PHE C 342 
 TRP   0.033   0.002   TRP C 303 
 HIS   0.015   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9716)
  covalent geometry    : angle       0.69695 (13132)
  hydrogen bonds       : bond        0.04022 (  529)
  hydrogen bonds       : angle       4.64722 ( 1554)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1992.91 seconds
wall clock time: 35 minutes 31.70 seconds (2131.70 seconds total)