Starting phenix.real_space_refine
on Fri Mar 14 04:38:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkb_61550/03_2025/9jkb_61550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkb_61550/03_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_61550/03_2025/9jkb_61550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkb_61550/03_2025/9jkb_61550.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jkb_61550/03_2025/9jkb_61550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkb_61550/03_2025/9jkb_61550.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.63, per 1000 atoms: 0.80
  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.96
  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: 3.17

  Time building geometry restraints manager: 2.68 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:             26.200
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.650
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.500
-------------------------------------------------------------------------------
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= 0.211
  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 : 7.81
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (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
 TRP   0.009   0.001   TRP A 167 
 HIS   0.008   0.001   HIS C 355 
 PHE   0.025   0.001   PHE A 402 
 TYR   0.035   0.001   TYR A 570 
 ARG   0.004   0.000   ARG A 707 

*********************** 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  : 1.191 
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: 0.2425
  time to fit residues: 79.9934
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  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.0040
   chunk 87 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    0.2980
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   overall best weight:    0.3770

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.129562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.095240 restraints weight = 26312.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.095049 restraints weight = 14460.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.095736 restraints weight = 12069.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2007

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= 0.190
  Angle     :  0.634  11.543  13132  Z= 0.324
  Chirality :  0.042   0.154   1466
  Planarity :  0.004   0.059   1685
  Dihedral  :  4.146  21.913   1267
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.07 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1165
  helix:  0.89 (0.19), residues: 700
  sheet: -2.02 (0.82), residues: 33
  loop : -1.21 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 303 
 HIS   0.010   0.001   HIS A 524 
 PHE   0.024   0.002   PHE A 402 
 TYR   0.029   0.002   TYR A 570 
 ARG   0.004   0.000   ARG D 100 

*********************** 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
  202 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  315 ASP cc_start: 0.5397 (m-30) cc_final: 0.5091 (m-30)
REVERT: C  370 PHE cc_start: 0.7501 (m-10) cc_final: 0.7222 (m-10)
REVERT: C  376 TRP cc_start: 0.6225 (t-100) cc_final: 0.5765 (t-100)
REVERT: A   43 MET cc_start: 0.8966 (tpp) cc_final: 0.8744 (tpp)
REVERT: A  199 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8202 (tpp-160)
REVERT: A  409 THR cc_start: 0.8627 (p) cc_final: 0.8336 (t)
REVERT: A  566 PHE cc_start: 0.8499 (t80) cc_final: 0.8119 (t80)
REVERT: A  632 LYS cc_start: 0.9343 (ptpt) cc_final: 0.9126 (ptpp)
REVERT: A  664 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8682 (mppt)
REVERT: A  701 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8866 (tptt)
REVERT: A  719 MET cc_start: 0.4289 (tpp) cc_final: 0.4042 (tpp)
REVERT: B   14 PHE cc_start: 0.7748 (m-80) cc_final: 0.7515 (m-80)
REVERT: B   60 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8116 (tm-30)
REVERT: B  157 ASN cc_start: 0.8607 (p0) cc_final: 0.8350 (p0)
REVERT: R   25 LYS cc_start: 0.8008 (pttm) cc_final: 0.7763 (pttm)
REVERT: D   57 SER cc_start: 0.6530 (t) cc_final: 0.6198 (p)
REVERT: D   61 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7706 (mmm-85)
REVERT: D  133 ASP cc_start: 0.7437 (p0) cc_final: 0.6887 (t0)
  outliers start: 17
  outliers final: 8
  residues processed: 193
  average time/residue: 0.2168
  time to fit residues: 58.8146
Evaluate side-chains
  154 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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  253 GLN
Chi-restraints excluded: chain B residue   34 LEU
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 53 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 78 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 HIS
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.131164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.093529 restraints weight = 25089.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.093637 restraints weight = 12712.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.094549 restraints weight = 9892.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9716  Z= 0.226
  Angle     :  0.615  11.321  13132  Z= 0.317
  Chirality :  0.041   0.176   1466
  Planarity :  0.004   0.057   1685
  Dihedral  :  4.019  22.454   1267
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.20 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1165
  helix:  1.08 (0.19), residues: 692
  sheet: -2.35 (0.88), residues: 28
  loop : -1.11 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 303 
 HIS   0.016   0.002   HIS C 309 
 PHE   0.023   0.002   PHE C 342 
 TYR   0.026   0.002   TYR A 377 
 ARG   0.004   0.000   ARG D 100 

*********************** 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
  185 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 PHE cc_start: 0.3061 (OUTLIER) cc_final: 0.2596 (m-80)
REVERT: C  315 ASP cc_start: 0.5362 (m-30) cc_final: 0.5041 (m-30)
REVERT: C  351 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7848 (p0)
REVERT: C  370 PHE cc_start: 0.7708 (m-10) cc_final: 0.7315 (m-10)
REVERT: A  261 MET cc_start: 0.8808 (mtp) cc_final: 0.8378 (ttt)
REVERT: A  409 THR cc_start: 0.8627 (p) cc_final: 0.8306 (t)
REVERT: A  566 PHE cc_start: 0.8551 (t80) cc_final: 0.8344 (t80)
REVERT: A  632 LYS cc_start: 0.9371 (ptpt) cc_final: 0.9118 (ptpp)
REVERT: A  640 LEU cc_start: 0.9199 (mt) cc_final: 0.8603 (pp)
REVERT: A  664 LYS cc_start: 0.9247 (mmtm) cc_final: 0.8734 (mppt)
REVERT: A  701 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8875 (tptt)
REVERT: A  719 MET cc_start: 0.4684 (tpp) cc_final: 0.4482 (tpp)
REVERT: B   60 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: B  157 ASN cc_start: 0.8656 (p0) cc_final: 0.8422 (p0)
REVERT: D   57 SER cc_start: 0.6762 (t) cc_final: 0.6460 (m)
REVERT: D   61 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7873 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8666 (p-90) cc_final: 0.8221 (p-90)
REVERT: D  133 ASP cc_start: 0.7525 (p0) cc_final: 0.6857 (t0)
  outliers start: 27
  outliers final: 19
  residues processed: 172
  average time/residue: 0.2011
  time to fit residues: 49.9252
Evaluate side-chains
  164 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
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  465 PHE
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  539 VAL
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 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 60 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 92 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 253 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.131505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.094175 restraints weight = 24755.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.094429 restraints weight = 12468.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.095342 restraints weight = 9768.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9716  Z= 0.200
  Angle     :  0.611  10.830  13132  Z= 0.311
  Chirality :  0.041   0.225   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  3.987  21.392   1267
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.91 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1165
  helix:  1.15 (0.19), residues: 694
  sheet: -2.16 (0.76), residues: 33
  loop : -1.09 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 303 
 HIS   0.012   0.001   HIS C 309 
 PHE   0.025   0.002   PHE C 342 
 TYR   0.033   0.002   TYR A 570 
 ARG   0.004   0.000   ARG A 745 

*********************** 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
  192 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 PHE cc_start: 0.3041 (OUTLIER) cc_final: 0.2571 (m-80)
REVERT: C  315 ASP cc_start: 0.5307 (m-30) cc_final: 0.4919 (m-30)
REVERT: C  351 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7723 (p0)
REVERT: A  199 ARG cc_start: 0.8509 (tpp-160) cc_final: 0.8264 (tpp-160)
REVERT: A  253 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (mp-120)
REVERT: A  261 MET cc_start: 0.8760 (mtp) cc_final: 0.8494 (ttt)
REVERT: A  305 THR cc_start: 0.9149 (m) cc_final: 0.8677 (p)
REVERT: A  409 THR cc_start: 0.8625 (p) cc_final: 0.8277 (t)
REVERT: A  566 PHE cc_start: 0.8572 (t80) cc_final: 0.8369 (t80)
REVERT: A  570 TYR cc_start: 0.7515 (p90) cc_final: 0.7300 (p90)
REVERT: A  640 LEU cc_start: 0.9210 (mt) cc_final: 0.8740 (pp)
REVERT: A  664 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8727 (mppt)
REVERT: A  701 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8882 (tptt)
REVERT: A  719 MET cc_start: 0.4517 (tpp) cc_final: 0.4268 (tpp)
REVERT: B   60 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: B  100 LEU cc_start: 0.8268 (tt) cc_final: 0.7882 (tp)
REVERT: B  157 ASN cc_start: 0.8659 (p0) cc_final: 0.8429 (p0)
REVERT: D   57 SER cc_start: 0.6593 (t) cc_final: 0.6381 (m)
REVERT: D   61 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7853 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8667 (p-90) cc_final: 0.8220 (p-90)
REVERT: D  133 ASP cc_start: 0.7575 (p0) cc_final: 0.6893 (t0)
  outliers start: 28
  outliers final: 19
  residues processed: 177
  average time/residue: 0.1924
  time to fit residues: 49.2746
Evaluate side-chains
  167 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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  253 GLN
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   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    0.3980
   chunk 114 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 253 GLN
A 343 HIS
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.123733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.088240 restraints weight = 23880.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.086734 restraints weight = 14102.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.087541 restraints weight = 11983.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9716  Z= 0.239
  Angle     :  0.625   9.888  13132  Z= 0.319
  Chirality :  0.042   0.195   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  3.967  22.782   1267
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.90 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.24), residues: 1165
  helix:  1.18 (0.19), residues: 695
  sheet: -2.17 (0.77), residues: 33
  loop : -1.05 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 303 
 HIS   0.011   0.001   HIS C 309 
 PHE   0.021   0.002   PHE C 342 
 TYR   0.026   0.002   TYR A 278 
 ARG   0.005   0.000   ARG A 745 

*********************** 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
  181 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  289 PHE cc_start: 0.2979 (OUTLIER) cc_final: 0.2508 (m-80)
REVERT: C  315 ASP cc_start: 0.5401 (m-30) cc_final: 0.5036 (m-30)
REVERT: C  342 PHE cc_start: 0.8667 (m-10) cc_final: 0.8385 (m-10)
REVERT: C  351 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7671 (p0)
REVERT: C  357 TRP cc_start: 0.8056 (p-90) cc_final: 0.7452 (p-90)
REVERT: C  370 PHE cc_start: 0.7577 (m-10) cc_final: 0.7351 (m-10)
REVERT: A   37 MET cc_start: 0.9067 (ppp) cc_final: 0.8864 (ppp)
REVERT: A  199 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8209 (tpp-160)
REVERT: A  305 THR cc_start: 0.9177 (m) cc_final: 0.8743 (p)
REVERT: A  409 THR cc_start: 0.8628 (p) cc_final: 0.8298 (t)
REVERT: A  566 PHE cc_start: 0.8541 (t80) cc_final: 0.8175 (t80)
REVERT: A  633 MET cc_start: 0.8778 (tpt) cc_final: 0.8005 (pmm)
REVERT: A  640 LEU cc_start: 0.9194 (mt) cc_final: 0.8756 (pp)
REVERT: A  664 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8696 (mppt)
REVERT: A  701 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8882 (tptt)
REVERT: A  719 MET cc_start: 0.4364 (tpp) cc_final: 0.4152 (tpp)
REVERT: B   60 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: B  157 ASN cc_start: 0.8594 (p0) cc_final: 0.8350 (p0)
REVERT: D   61 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7759 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8560 (p-90) cc_final: 0.7986 (p-90)
REVERT: D  133 ASP cc_start: 0.7417 (p0) cc_final: 0.6741 (t0)
REVERT: D  145 MET cc_start: 0.7863 (tmm) cc_final: 0.7634 (tmm)
  outliers start: 29
  outliers final: 21
  residues processed: 166
  average time/residue: 0.2118
  time to fit residues: 51.0333
Evaluate side-chains
  162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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   84 VAL
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  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   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
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 54 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0070
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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  35 GLN
A 253 GLN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.123347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.093582 restraints weight = 24382.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.093284 restraints weight = 24973.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.094015 restraints weight = 23060.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9716  Z= 0.208
  Angle     :  0.616  10.930  13132  Z= 0.314
  Chirality :  0.041   0.177   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  3.936  22.125   1267
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.04 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1165
  helix:  1.26 (0.19), residues: 694
  sheet: -2.09 (0.77), residues: 33
  loop : -1.03 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 303 
 HIS   0.012   0.001   HIS A 524 
 PHE   0.023   0.002   PHE A 498 
 TYR   0.027   0.002   TYR A 570 
 ARG   0.005   0.000   ARG A 745 

*********************** 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
  182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6085 (p90) cc_final: 0.5722 (p90)
REVERT: C  289 PHE cc_start: 0.2523 (OUTLIER) cc_final: 0.2031 (m-80)
REVERT: C  315 ASP cc_start: 0.5355 (m-30) cc_final: 0.5069 (m-30)
REVERT: C  357 TRP cc_start: 0.7522 (p-90) cc_final: 0.7286 (p-90)
REVERT: A  199 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8272 (tpp-160)
REVERT: A  409 THR cc_start: 0.8584 (p) cc_final: 0.8251 (t)
REVERT: A  640 LEU cc_start: 0.9009 (mt) cc_final: 0.8690 (pp)
REVERT: A  664 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8619 (mppt)
REVERT: B   60 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: B  100 LEU cc_start: 0.8287 (tt) cc_final: 0.7824 (tp)
REVERT: B  157 ASN cc_start: 0.8371 (p0) cc_final: 0.8164 (p0)
REVERT: D   61 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7814 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8146 (p-90) cc_final: 0.7616 (p-90)
REVERT: D  133 ASP cc_start: 0.7126 (p0) cc_final: 0.6567 (t0)
REVERT: D  140 MET cc_start: 0.8209 (mtm) cc_final: 0.7863 (ptp)
REVERT: D  145 MET cc_start: 0.7789 (tmm) cc_final: 0.7516 (tmm)
  outliers start: 33
  outliers final: 23
  residues processed: 170
  average time/residue: 0.2012
  time to fit residues: 48.9346
Evaluate side-chains
  160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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   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  253 GLN
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   34 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  131 THR
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 83 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 113 optimal weight:    0.1980
   chunk 98 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 3 optimal weight:   30.0000
   chunk 43 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 253 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.123358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.087646 restraints weight = 24308.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.086094 restraints weight = 15017.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.086575 restraints weight = 13097.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9716  Z= 0.233
  Angle     :  0.646  12.297  13132  Z= 0.330
  Chirality :  0.042   0.176   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.006  21.923   1267
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.24), residues: 1165
  helix:  1.18 (0.20), residues: 697
  sheet: -2.22 (0.76), residues: 33
  loop : -1.00 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 303 
 HIS   0.017   0.001   HIS A 524 
 PHE   0.019   0.002   PHE C 370 
 TYR   0.038   0.002   TYR A 570 
 ARG   0.005   0.000   ARG A 745 

*********************** 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
  181 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6501 (p90) cc_final: 0.6067 (p90)
REVERT: C  289 PHE cc_start: 0.3056 (OUTLIER) cc_final: 0.2537 (m-80)
REVERT: C  315 ASP cc_start: 0.5400 (m-30) cc_final: 0.5042 (m-30)
REVERT: C  357 TRP cc_start: 0.7905 (p-90) cc_final: 0.7470 (p-90)
REVERT: C  370 PHE cc_start: 0.7596 (m-10) cc_final: 0.7383 (m-10)
REVERT: A  199 ARG cc_start: 0.8369 (tpp-160) cc_final: 0.8134 (tpp-160)
REVERT: A  261 MET cc_start: 0.8333 (ttt) cc_final: 0.7961 (ttt)
REVERT: A  322 MET cc_start: 0.8990 (tpt) cc_final: 0.8589 (tpt)
REVERT: A  409 THR cc_start: 0.8589 (p) cc_final: 0.8259 (t)
REVERT: A  508 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7882 (m-80)
REVERT: A  633 MET cc_start: 0.8782 (tpt) cc_final: 0.8016 (pmm)
REVERT: A  640 LEU cc_start: 0.9181 (mt) cc_final: 0.8796 (pp)
REVERT: A  664 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8710 (mppt)
REVERT: B   60 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: B  100 LEU cc_start: 0.8281 (tt) cc_final: 0.7862 (tp)
REVERT: B  157 ASN cc_start: 0.8592 (p0) cc_final: 0.8330 (p0)
REVERT: D   61 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7789 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8526 (p-90) cc_final: 0.7941 (p-90)
REVERT: D  133 ASP cc_start: 0.7483 (p0) cc_final: 0.6776 (t0)
REVERT: D  145 MET cc_start: 0.7838 (tmm) cc_final: 0.7567 (tmm)
  outliers start: 37
  outliers final: 26
  residues processed: 169
  average time/residue: 0.2105
  time to fit residues: 50.9575
Evaluate side-chains
  163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
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   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  253 GLN
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  508 PHE
Chi-restraints excluded: chain A residue  535 PHE
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   34 LEU
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 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 87 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   chunk 24 optimal weight:    0.4980
   chunk 90 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 253 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.123059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.093658 restraints weight = 24558.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.092780 restraints weight = 28538.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.093527 restraints weight = 26026.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9716  Z= 0.226
  Angle     :  0.657  11.499  13132  Z= 0.332
  Chirality :  0.042   0.218   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.021  23.244   1267
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.56 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1165
  helix:  1.16 (0.19), residues: 698
  sheet: -2.29 (0.73), residues: 33
  loop : -0.95 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C 303 
 HIS   0.015   0.001   HIS A 524 
 PHE   0.017   0.002   PHE C 370 
 TYR   0.020   0.002   TYR A 278 
 ARG   0.005   0.000   ARG A 745 

*********************** 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
  182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6097 (p90) cc_final: 0.5527 (p90)
REVERT: C  289 PHE cc_start: 0.2767 (OUTLIER) cc_final: 0.2268 (m-80)
REVERT: C  315 ASP cc_start: 0.5303 (m-30) cc_final: 0.4985 (m-30)
REVERT: A  127 ARG cc_start: 0.8461 (ttt-90) cc_final: 0.8191 (ttt-90)
REVERT: A  199 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8325 (tpp-160)
REVERT: A  261 MET cc_start: 0.8290 (ttt) cc_final: 0.7865 (ttt)
REVERT: A  322 MET cc_start: 0.9051 (tpt) cc_final: 0.8466 (tpt)
REVERT: A  331 ASP cc_start: 0.7995 (t0) cc_final: 0.7741 (t0)
REVERT: A  409 THR cc_start: 0.8603 (p) cc_final: 0.8314 (t)
REVERT: A  508 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7818 (m-80)
REVERT: A  633 MET cc_start: 0.8354 (tpt) cc_final: 0.7817 (pmm)
REVERT: A  640 LEU cc_start: 0.9028 (mt) cc_final: 0.8735 (pp)
REVERT: A  664 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8649 (mppt)
REVERT: B   60 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: B  100 LEU cc_start: 0.8335 (tt) cc_final: 0.7915 (tp)
REVERT: B  157 ASN cc_start: 0.8397 (p0) cc_final: 0.8145 (p0)
REVERT: D   61 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7862 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8198 (p-90) cc_final: 0.7687 (p-90)
REVERT: D  133 ASP cc_start: 0.7231 (p0) cc_final: 0.6628 (t0)
  outliers start: 37
  outliers final: 26
  residues processed: 171
  average time/residue: 0.2042
  time to fit residues: 49.9292
Evaluate side-chains
  161 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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   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  253 GLN
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  508 PHE
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue   34 LEU
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0770
   chunk 36 optimal weight:    0.3980
   overall best weight:    1.0342

-------------------------------------------------------------------------------
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 253 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.122106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.085657 restraints weight = 24080.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.084909 restraints weight = 14583.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.085199 restraints weight = 13099.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   9716  Z= 0.295
  Angle     :  0.700  12.401  13132  Z= 0.353
  Chirality :  0.044   0.207   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.116  23.418   1267
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.64 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.61 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1165
  helix:  1.12 (0.20), residues: 697
  sheet: -2.62 (0.73), residues: 33
  loop : -0.95 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 303 
 HIS   0.014   0.001   HIS A 524 
 PHE   0.017   0.002   PHE A 402 
 TYR   0.044   0.002   TYR A 570 
 ARG   0.003   0.000   ARG A 745 

*********************** 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
  166 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6476 (p90) cc_final: 0.6042 (p90)
REVERT: C  289 PHE cc_start: 0.3272 (OUTLIER) cc_final: 0.2729 (m-80)
REVERT: C  315 ASP cc_start: 0.5349 (m-30) cc_final: 0.4974 (m-30)
REVERT: A  199 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.8172 (tpp-160)
REVERT: A  261 MET cc_start: 0.8303 (ttt) cc_final: 0.7856 (ttt)
REVERT: A  322 MET cc_start: 0.9123 (tpt) cc_final: 0.8523 (tpt)
REVERT: A  331 ASP cc_start: 0.7896 (t0) cc_final: 0.7632 (t0)
REVERT: A  508 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7889 (m-80)
REVERT: A  521 PHE cc_start: 0.8849 (t80) cc_final: 0.8420 (m-80)
REVERT: A  608 MET cc_start: 0.8702 (mpp) cc_final: 0.8494 (mpp)
REVERT: A  633 MET cc_start: 0.8832 (tpt) cc_final: 0.8055 (pmm)
REVERT: A  664 LYS cc_start: 0.9280 (mmtm) cc_final: 0.8735 (mppt)
REVERT: B   60 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: R   25 LYS cc_start: 0.8475 (pttm) cc_final: 0.8201 (pttm)
REVERT: D   61 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7629 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8500 (p-90) cc_final: 0.8113 (p-90)
REVERT: D  133 ASP cc_start: 0.7432 (p0) cc_final: 0.6743 (t0)
  outliers start: 32
  outliers final: 26
  residues processed: 155
  average time/residue: 0.1992
  time to fit residues: 44.2807
Evaluate side-chains
  158 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  203 LEU
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  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  508 PHE
Chi-restraints excluded: chain A residue  535 PHE
Chi-restraints excluded: chain A residue  537 ILE
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 B residue   34 LEU
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 58 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
C 229 HIS
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.124020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.088213 restraints weight = 24118.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.087012 restraints weight = 13997.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.087769 restraints weight = 11901.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9716  Z= 0.199
  Angle     :  0.687  11.269  13132  Z= 0.343
  Chirality :  0.042   0.208   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.110  23.053   1267
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.65 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1165
  helix:  1.11 (0.19), residues: 699
  sheet: -3.19 (0.74), residues: 27
  loop : -0.95 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C 303 
 HIS   0.013   0.001   HIS A 524 
 PHE   0.030   0.002   PHE A 498 
 TYR   0.031   0.002   TYR A 278 
 ARG   0.003   0.000   ARG A 745 

********************** 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: 25
    poor density    : 138
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 PHE cc_start: 0.6348 (p90) cc_final: 0.5838 (p90)
REVERT: C  289 PHE cc_start: 0.3058 (OUTLIER) cc_final: 0.2546 (m-80)
REVERT: C  315 ASP cc_start: 0.5391 (m-30) cc_final: 0.5026 (m-30)
REVERT: A   52 TYR cc_start: 0.8877 (t80) cc_final: 0.8665 (t80)
REVERT: A  261 MET cc_start: 0.8178 (ttt) cc_final: 0.7827 (ttt)
REVERT: A  322 MET cc_start: 0.9102 (tpt) cc_final: 0.8487 (tpt)
REVERT: A  331 ASP cc_start: 0.7872 (t0) cc_final: 0.7617 (t0)
REVERT: A  450 MET cc_start: 0.8696 (tpp) cc_final: 0.8396 (tpp)
REVERT: A  521 PHE cc_start: 0.8787 (t80) cc_final: 0.8417 (m-80)
REVERT: A  664 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8717 (mppt)
REVERT: B   60 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8033 (tm-30)
REVERT: B  100 LEU cc_start: 0.8142 (tt) cc_final: 0.7659 (tp)
REVERT: D   61 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7608 (mmm-85)
REVERT: D  115 TRP cc_start: 0.8468 (p-90) cc_final: 0.8099 (p-90)
REVERT: D  133 ASP cc_start: 0.7442 (p0) cc_final: 0.6758 (t0)
REVERT: D  145 MET cc_start: 0.7936 (tmm) cc_final: 0.7499 (tmm)
  outliers start: 25
  outliers final: 22
  residues processed: 154
  average time/residue: 0.2845
  time to fit residues: 62.6032
Evaluate side-chains
  153 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
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  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  535 PHE
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain B residue   34 LEU
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0000
   chunk 32 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 74 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 58 optimal weight:    0.1980
   chunk 93 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.3984

-------------------------------------------------------------------------------
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**
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 = 0.3980 r_free = 0.3980 target = 0.124672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.088740 restraints weight = 23979.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.087401 restraints weight = 13826.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.088321 restraints weight = 11929.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
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   0.065   9716  Z= 0.196
  Angle     :  0.691  10.827  13132  Z= 0.343
  Chirality :  0.042   0.209   1466
  Planarity :  0.004   0.058   1685
  Dihedral  :  4.064  22.706   1267
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.13 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1165
  helix:  1.08 (0.19), residues: 706
  sheet: -2.99 (0.77), residues: 27
  loop : -0.92 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C 303 
 HIS   0.012   0.001   HIS A 524 
 PHE   0.029   0.001   PHE A 498 
 TYR   0.045   0.002   TYR A 570 
 ARG   0.004   0.000   ARG A 745 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3855.52 seconds
wall clock time: 69 minutes 10.82 seconds (4150.82 seconds total)