Starting phenix.real_space_refine
on Wed Aug  5 21:14:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w9f_65773/08_2026/9w9f_65773.map"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.127
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     150      5.49       5
     S      30      5.16       5
     C    6691      2.51       5
     N    2078      2.21       5
     O    2622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11571
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4375
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 508}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1594
          Classifications: {'RNA': 75}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 12, 'rna3p': 62}
    Chain: "B"
      Number of atoms: 4008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 4008
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 30, 'TRANS': 465}
    Chain: "S"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1594
          Classifications: {'RNA': 75}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 12, 'rna3p': 62}
  Time building chain proxies: 2.52, per 1000 atoms: 0.22
  Number of scatterers: 11571
  At special positions: 0
  Unit cell: (96.28, 99.6, 136.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P     150     15.00
     O    2622      8.00
     N    2078      7.00
     C    6691      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 349.4 milliseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1946

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      39.4% alpha, 17.6% beta
      45 base pairs and 74 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 80
      removed outlier: 4.146A  pdb=" N   LYS A  65 " --> pdb=" O   ARG A  61 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 102
    Processing helix  chain 'A' and resid 104 through 111
      removed outlier: 3.565A  pdb=" N   TYR A 111 " --> pdb=" O   MET A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 191
    Processing helix  chain 'A' and resid 239 through 244
    Processing helix  chain 'A' and resid 247 through 253
    Processing helix  chain 'A' and resid 261 through 268
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 275 through 300
      removed outlier: 3.513A  pdb=" N   CYS A 289 " --> pdb=" O   GLN A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 346
      removed outlier: 4.503A  pdb=" N   ALA A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 406
      removed outlier: 4.189A  pdb=" N   MET A 388 " --> pdb=" O   HIS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 3.957A  pdb=" N   ILE A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN A 417 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 445
    Processing helix  chain 'A' and resid 461 through 476
    Processing helix  chain 'A' and resid 526 through 538
    Processing helix  chain 'A' and resid 540 through 543
    Processing helix  chain 'A' and resid 544 through 554
      removed outlier: 3.563A  pdb=" N   PHE A 551 " --> pdb=" O   TYR A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 577 through 582
      removed outlier: 3.661A  pdb=" N   ALA A 581 " --> pdb=" O   ASN A 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 191
    Processing helix  chain 'B' and resid 239 through 244
    Processing helix  chain 'B' and resid 247 through 252
    Processing helix  chain 'B' and resid 261 through 268
    Processing helix  chain 'B' and resid 268 through 275
    Processing helix  chain 'B' and resid 275 through 300
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 385 through 407
      removed outlier: 3.986A  pdb=" N   LEU B 389 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA B 394 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY B 405 " --> pdb=" O   LYS B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 418
      removed outlier: 3.845A  pdb=" N   GLN B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 444
    Processing helix  chain 'B' and resid 461 through 477
    Processing helix  chain 'B' and resid 526 through 538
    Processing helix  chain 'B' and resid 540 through 543
      removed outlier: 3.522A  pdb=" N   THR B 543 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 540 through 543'
    Processing helix  chain 'B' and resid 544 through 554
    Processing helix  chain 'B' and resid 565 through 574
    Processing helix  chain 'B' and resid 577 through 581
    Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145
      removed outlier: 4.208A  pdb=" N   PHE A 144 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   VAL A 200 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   ARG A 201 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 9.181A  pdb=" N   LEU A 221 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   GLN A 171 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   VAL A 223 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   VAL A 173 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   GLN A 225 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 11.650A  pdb=" N   HIS A 175 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   PHE A 160 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   ILE A 151 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL A 162 " --> pdb=" O   HIS A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303
      removed outlier: 6.218A  pdb=" N   ILE A 302 " --> pdb=" O   TYR A 352 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   ILE A 354 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   HIS A 558 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY A 562 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER A 519 " --> pdb=" O   GLY A 562 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A 564 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ILE A 517 " --> pdb=" O   GLY A 564 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   GLU A 516 " --> pdb=" O   ILE A 512 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ILE A 512 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL A 518 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   ILE A 432 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310
      removed outlier: 4.428A  pdb=" N   GLN B 322 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 152
      removed outlier: 5.280A  pdb=" N   LEU B 148 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   ARG B 164 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
      removed outlier: 10.278A  pdb=" N   THR B 169 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 10.039A  pdb=" N   LEU B 221 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   GLN B 171 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 8.412A  pdb=" N   VAL B 223 " --> pdb=" O   GLN B 171 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   VAL B 173 " --> pdb=" O   VAL B 223 " (cutoff:3.500A)
      removed outlier: 10.230A  pdb=" N   GLN B 225 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ARG B 201 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ILE B 226 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ARG B 199 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL B 198 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA B 146 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 310
    Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 353
      removed outlier: 3.868A  pdb=" N   TYR B 372 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 353
      removed outlier: 4.378A  pdb=" N   HIS B 558 " --> pdb=" O   ARG B 523 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B 562 " --> pdb=" O   SER B 519 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 519 " --> pdb=" O   GLY B 562 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 564 " --> pdb=" O   ILE B 517 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE B 517 " --> pdb=" O   GLY B 564 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   GLU B 516 " --> pdb=" O   ILE B 512 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ILE B 512 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 497 through 498
      removed outlier: 3.958A  pdb=" N   ASP B 498 " --> pdb=" O   PHE B 504 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   PHE B 504 " --> pdb=" O   ASP B 498 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    344 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      118 hydrogen bonds
      200 hydrogen bond angles
      0 basepair planarities
      45 basepair parallelities
      74 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3184
        1.34 -     1.46: 2899
        1.46 -     1.57: 5685
        1.57 -     1.69: 298
        1.69 -     1.81: 56
  Bond restraints: 12122
  Sorted by residual:
  bond pdb=" N   VAL A 229 "
       pdb=" CA  VAL A 229 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.14e-02 7.69e+03 9.62e+00
  bond pdb=" N   VAL A 219 "
       pdb=" CA  VAL A 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.19e-02 7.06e+03 9.61e+00
  bond pdb=" N   GLU B 382 "
       pdb=" CA  GLU B 382 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.23e-02 6.61e+03 9.53e+00
  bond pdb=" N   ILE B 381 "
       pdb=" CA  ILE B 381 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.74e+00
  bond pdb=" N   VAL A 230 "
       pdb=" CA  VAL A 230 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.17e+00
  ... (remaining 12117 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 16001
        1.53 -     3.07: 940
        3.07 -     4.60: 118
        4.60 -     6.13: 38
        6.13 -     7.67: 16
  Bond angle restraints: 17113
  Sorted by residual:
  angle pdb=" C3'   A S  46 "
        pdb=" C2'   A S  46 "
        pdb=" C1'   A S  46 "
      ideal   model   delta    sigma   weight residual
     101.30  104.18   -2.88 7.00e-01 2.04e+00 1.69e+01
  angle pdb=" C2'   G S  73 "
        pdb=" C1'   G S  73 "
        pdb=" N9    G S  73 "
      ideal   model   delta    sigma   weight residual
     112.00  116.07   -4.07 1.10e+00 8.26e-01 1.37e+01
  angle pdb=" O5'   C R  49 "
        pdb=" C5'   C R  49 "
        pdb=" C4'   C R  49 "
      ideal   model   delta    sigma   weight residual
     109.40  112.25   -2.85 8.00e-01 1.56e+00 1.27e+01
  angle pdb=" O5'   C S  12 "
        pdb=" C5'   C S  12 "
        pdb=" C4'   C S  12 "
      ideal   model   delta    sigma   weight residual
     109.40  112.18   -2.78 8.00e-01 1.56e+00 1.21e+01
  angle pdb=" O5'   C R  20A"
        pdb=" C5'   C R  20A"
        pdb=" C4'   C R  20A"
      ideal   model   delta    sigma   weight residual
     109.40  112.15   -2.75 8.00e-01 1.56e+00 1.18e+01
  ... (remaining 17108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.98: 6869
       26.98 -    53.96: 477
       53.96 -    80.95: 292
       80.95 -   107.93: 4
      107.93 -   134.91: 1
  Dihedral angle restraints: 7643
    sinusoidal: 4638
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" C5'   C R  48 "
           pdb=" C4'   C R  48 "
           pdb=" C3'   C R  48 "
           pdb=" O3'   C R  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  108.26   38.74     1      8.00e+00 1.56e-02 3.30e+01
  dihedral pdb=" O4'   C R  48 "
           pdb=" C4'   C R  48 "
           pdb=" C3'   C R  48 "
           pdb=" C2'   C R  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00   -7.47   31.47     1      8.00e+00 1.56e-02 2.21e+01
  dihedral pdb=" C3'   C R  48 "
           pdb=" C4'   C R  48 "
           pdb=" O4'   C R  48 "
           pdb=" C1'   C R  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   26.91  -28.91     1      8.00e+00 1.56e-02 1.87e+01
  ... (remaining 7640 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1820
       0.117 -    0.234: 150
       0.234 -    0.351: 0
       0.351 -    0.468: 10
       0.468 -    0.584: 10
  Chirality restraints: 1990
  Sorted by residual:
  chirality pdb=" P     U R   1 "
            pdb=" OP1   U R   1 "
            pdb=" OP2   U R   1 "
            pdb=" O5'   U R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.99   -0.58 2.00e-01 2.50e+01 8.54e+00
  chirality pdb=" P     U S   1 "
            pdb=" OP1   U S   1 "
            pdb=" OP2   U S   1 "
            pdb=" O5'   U S   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.77e+00
  chirality pdb=" CG  LEU A 228 "
            pdb=" CB  LEU A 228 "
            pdb=" CD1 LEU A 228 "
            pdb=" CD2 LEU A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 6.90e+00
  ... (remaining 1987 not shown)

  Planarity restraints: 1692
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 293 "    0.208 9.50e-02 1.11e+02   9.31e-02 5.45e+00
        pdb=" NE  ARG B 293 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 293 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 293 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 293 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G S  73 "    0.031 2.00e-02 2.50e+03   1.34e-02 5.36e+00
        pdb=" N9    G S  73 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8    G S  73 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G S  73 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G S  73 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G S  73 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G S  73 "    0.010 2.00e-02 2.50e+03
        pdb=" N1    G S  73 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G S  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G S  73 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G S  73 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G S  73 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 124 "    0.192 9.50e-02 1.11e+02   8.63e-02 5.22e+00
        pdb=" NE  ARG A 124 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 124 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 124 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 124 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1689 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3176
        2.82 -     3.34: 11516
        3.34 -     3.86: 22414
        3.86 -     4.38: 26393
        4.38 -     4.90: 37883
  Nonbonded interactions: 101382
  Sorted by model distance:
  nonbonded pdb=" CA  ILE A 197 "
            pdb=" CG1 VAL A 229 "
     model   vdw
     2.296 3.890
  nonbonded pdb=" O2'   C S  67 "
            pdb=" O4'   G S  68 "
     model   vdw
     2.473 3.040
  nonbonded pdb=" N   GLU B 410 "
            pdb=" OE1 GLU B 410 "
     model   vdw
     2.528 3.120
  nonbonded pdb=" O   SER A 196 "
            pdb=" OG  SER A 196 "
     model   vdw
     2.533 3.040
  nonbonded pdb=" N   GLU B 421 "
            pdb=" OE1 GLU B 421 "
     model   vdw
     2.537 3.120
  ... (remaining 101377 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 102 through 597)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'R'
  selection = chain 'S'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.130
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
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      :  0.004   0.059  12122  Z= 0.248
  Angle     :  0.804   7.668  17113  Z= 0.509
  Chirality :  0.071   0.584   1990
  Planarity :  0.006   0.093   1692
  Dihedral  : 19.812 134.912   5697
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.69 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1031
  helix:  0.76 (0.26), residues: 371
  sheet: -0.39 (0.46), residues: 111
  loop : -0.15 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 122 
 TYR   0.021   0.002   TYR B 547 
 PHE   0.032   0.002   PHE A 292 
 TRP   0.011   0.001   TRP A 553 
 HIS   0.010   0.002   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.25 (12122)
  covalent geometry    : angle       0.80355 /  0.51 (17113)
  hydrogen bonds       : bond        0.12936 /  8.85 (  458)
  hydrogen bonds       : angle       7.25454 /  5.22 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 242
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 HIS cc_start: 0.5252 (m170) cc_final: 0.4952 (m170)
REVERT: A  231 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7106 (p-80)
REVERT: A  529 MET cc_start: 0.8539 (ttm) cc_final: 0.8073 (tpt)
REVERT: A  570 MET cc_start: 0.6506 (ttp) cc_final: 0.5588 (tmm)
REVERT: B  129 ARG cc_start: 0.7062 (ttp-170) cc_final: 0.6596 (mmp80)
REVERT: B  167 LEU cc_start: 0.7673 (mp) cc_final: 0.6923 (mp)
REVERT: B  260 LEU cc_start: 0.7904 (tp) cc_final: 0.7665 (tt)
REVERT: B  283 ARG cc_start: 0.8273 (ttt180) cc_final: 0.7879 (ttt180)
REVERT: B  302 ILE cc_start: 0.8942 (mm) cc_final: 0.8648 (mp)
REVERT: B  362 ASN cc_start: 0.6701 (t0) cc_final: 0.6413 (t0)
REVERT: B  376 ASP cc_start: 0.6937 (m-30) cc_final: 0.6577 (m-30)
REVERT: B  480 TYR cc_start: 0.6546 (t80) cc_final: 0.6239 (t80)
REVERT: B  511 PHE cc_start: 0.6544 (m-80) cc_final: 0.6089 (m-10)
REVERT: B  530 LEU cc_start: 0.8562 (tp) cc_final: 0.8306 (tt)
REVERT: B  570 MET cc_start: 0.7826 (ttp) cc_final: 0.7585 (ttt)
  outliers start: 7
  outliers final: 2
  residues processed: 249
  average time/residue: 0.1346
  time to fit residues: 44.9418
Evaluate side-chains
  134 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 HIS
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  166 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:   50.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   overall best weight:    5.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  64 GLN
** A  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 GLN
A 231 HIS
** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 386 HIS
** A 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 ASN
B 285 GLN
B 334 GLN
B 341 GLN
B 461 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.122342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.100501 restraints weight = 42740.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.102705 restraints weight = 24532.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.104168 restraints weight = 16747.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.105106 restraints weight = 13007.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.105580 restraints weight = 11052.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096  12122  Z= 0.274
  Angle     :  0.786  14.878  17113  Z= 0.408
  Chirality :  0.046   0.412   1990
  Planarity :  0.007   0.116   1692
  Dihedral  : 21.326 110.006   3561
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 14.32 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.25), residues: 1031
  helix:  0.57 (0.25), residues: 368
  sheet: -1.29 (0.39), residues: 135
  loop : -0.43 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 129 
 TYR   0.022   0.003   TYR A 241 
 PHE   0.029   0.004   PHE A 508 
 TRP   0.036   0.003   TRP B 553 
 HIS   0.009   0.002   HIS A 558 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00597 /  0.27 (12122)
  covalent geometry    : angle       0.78618 /  0.41 (17113)
  hydrogen bonds       : bond        0.06806 /  4.58 (  458)
  hydrogen bonds       : angle       6.42098 /  4.60 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 120
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.8815 (ptm) cc_final: 0.8557 (ptm)
REVERT: A  425 TRP cc_start: 0.7911 (OUTLIER) cc_final: 0.7650 (p-90)
REVERT: A  480 TYR cc_start: 0.8771 (t80) cc_final: 0.8347 (t80)
REVERT: A  529 MET cc_start: 0.8009 (ttm) cc_final: 0.7733 (tpt)
REVERT: A  570 MET cc_start: 0.7453 (ttp) cc_final: 0.6806 (tmm)
REVERT: B  283 ARG cc_start: 0.8106 (ttt90) cc_final: 0.7787 (ttt180)
REVERT: B  496 MET cc_start: 0.8251 (ttm) cc_final: 0.7695 (ttp)
REVERT: B  570 MET cc_start: 0.8483 (ttp) cc_final: 0.8274 (ttt)
REVERT: B  583 LEU cc_start: 0.8792 (tp) cc_final: 0.8532 (tp)
  outliers start: 47
  outliers final: 15
  residues processed: 155
  average time/residue: 0.1276
  time to fit residues: 27.2535
Evaluate side-chains
  116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  416 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:   30.0000
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:   50.0000
   chunk 100 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 231 HIS
** B 368 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 = 0.4339 r_free = 0.4339 target = 0.122472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.100532 restraints weight = 43245.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.102640 restraints weight = 24997.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.104072 restraints weight = 17340.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.104944 restraints weight = 13577.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.105570 restraints weight = 11595.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12122  Z= 0.194
  Angle     :  0.677  10.492  17113  Z= 0.356
  Chirality :  0.041   0.322   1990
  Planarity :  0.006   0.109   1692
  Dihedral  : 21.327 112.797   3555
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.62 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.25), residues: 1031
  helix:  0.44 (0.25), residues: 374
  sheet: -1.30 (0.40), residues: 125
  loop : -0.50 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 528 
 TYR   0.021   0.002   TYR B 547 
 PHE   0.025   0.003   PHE A 292 
 TRP   0.016   0.002   TRP B 553 
 HIS   0.008   0.001   HIS B 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.19 (12122)
  covalent geometry    : angle       0.67725 /  0.36 (17113)
  hydrogen bonds       : bond        0.06137 /  4.12 (  458)
  hydrogen bonds       : angle       6.14756 /  4.41 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.8769 (ptm) cc_final: 0.8528 (ptm)
REVERT: A  407 TYR cc_start: 0.7076 (m-10) cc_final: 0.6866 (m-10)
REVERT: A  425 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7695 (p-90)
REVERT: A  480 TYR cc_start: 0.8728 (t80) cc_final: 0.8240 (t80)
REVERT: A  529 MET cc_start: 0.8238 (ttm) cc_final: 0.7769 (tpt)
REVERT: A  570 MET cc_start: 0.7385 (ttp) cc_final: 0.6821 (tmm)
REVERT: B  283 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7986 (ttt180)
REVERT: B  376 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7022 (m-30)
REVERT: B  393 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7413 (t70)
REVERT: B  570 MET cc_start: 0.8394 (ttp) cc_final: 0.8150 (ttt)
  outliers start: 40
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1178
  time to fit residues: 22.5563
Evaluate side-chains
  117 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  376 ASP
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 109 optimal weight:   50.0000
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:   40.0000
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  62 ASN
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 HIS
** B 368 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 = 0.4325 r_free = 0.4325 target = 0.121513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.099451 restraints weight = 43092.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.101538 restraints weight = 25231.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.102981 restraints weight = 17418.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.103853 restraints weight = 13600.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.104495 restraints weight = 11605.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12122  Z= 0.182
  Angle     :  0.643  10.794  17113  Z= 0.340
  Chirality :  0.041   0.283   1990
  Planarity :  0.006   0.103   1692
  Dihedral  : 21.369 113.632   3555
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.05 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.25), residues: 1031
  helix:  0.38 (0.25), residues: 366
  sheet: -1.36 (0.41), residues: 125
  loop : -0.54 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 528 
 TYR   0.026   0.002   TYR B 547 
 PHE   0.037   0.003   PHE B 282 
 TRP   0.009   0.001   TRP B 553 
 HIS   0.006   0.001   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 (12122)
  covalent geometry    : angle       0.64251 /  0.34 (17113)
  hydrogen bonds       : bond        0.05669 /  3.81 (  458)
  hydrogen bonds       : angle       6.06988 /  4.35 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 100
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.8738 (ptm) cc_final: 0.8534 (ptm)
REVERT: A  425 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7641 (p-90)
REVERT: A  529 MET cc_start: 0.8097 (ttm) cc_final: 0.7729 (tpt)
REVERT: A  570 MET cc_start: 0.7478 (ttp) cc_final: 0.6696 (tmm)
REVERT: B  376 ASP cc_start: 0.7243 (m-30) cc_final: 0.6896 (m-30)
REVERT: B  393 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7244 (t70)
REVERT: B  496 MET cc_start: 0.8088 (ttm) cc_final: 0.7261 (ttp)
REVERT: B  570 MET cc_start: 0.8304 (ttp) cc_final: 0.8000 (ttt)
  outliers start: 43
  outliers final: 27
  residues processed: 131
  average time/residue: 0.1137
  time to fit residues: 20.7796
Evaluate side-chains
  116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 54 optimal weight:   50.0000
   chunk 1 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 112 optimal weight:   40.0000
   chunk 106 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 HIS
B 285 GLN
** B 368 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 = 0.4331 r_free = 0.4331 target = 0.121361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.099400 restraints weight = 43181.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.101455 restraints weight = 24830.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.102893 restraints weight = 17211.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.103802 restraints weight = 13505.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.104255 restraints weight = 11547.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12122  Z= 0.160
  Angle     :  0.612   9.478  17113  Z= 0.324
  Chirality :  0.039   0.251   1990
  Planarity :  0.005   0.103   1692
  Dihedral  : 21.382 113.453   3555
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 19.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.82 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.25), residues: 1031
  helix:  0.35 (0.26), residues: 367
  sheet: -1.34 (0.42), residues: 124
  loop : -0.65 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 265 
 TYR   0.040   0.003   TYR B 547 
 PHE   0.024   0.003   PHE B 292 
 TRP   0.009   0.001   TRP A 188 
 HIS   0.007   0.001   HIS B 227 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (12122)
  covalent geometry    : angle       0.61208 /  0.32 (17113)
  hydrogen bonds       : bond        0.05297 /  3.52 (  458)
  hydrogen bonds       : angle       5.83360 /  4.18 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 96
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.6822 (ptt180) cc_final: 0.6404 (ptp90)
REVERT: A  185 MET cc_start: 0.8761 (ptm) cc_final: 0.8481 (ptm)
REVERT: A  285 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7485 (tp40)
REVERT: A  407 TYR cc_start: 0.7137 (m-80) cc_final: 0.6832 (m-10)
REVERT: A  425 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7602 (p-90)
REVERT: A  529 MET cc_start: 0.7899 (ttm) cc_final: 0.7613 (tpt)
REVERT: A  570 MET cc_start: 0.7431 (ttp) cc_final: 0.6874 (tmm)
REVERT: B  131 GLU cc_start: 0.7846 (pm20) cc_final: 0.7639 (pp20)
REVERT: B  271 LEU cc_start: 0.8036 (mt) cc_final: 0.7635 (mp)
REVERT: B  376 ASP cc_start: 0.6823 (m-30) cc_final: 0.6447 (m-30)
REVERT: B  393 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7367 (t70)
REVERT: B  496 MET cc_start: 0.8370 (ttm) cc_final: 0.7644 (ttp)
REVERT: B  513 ARG cc_start: 0.6646 (mmt180) cc_final: 0.6385 (tpt170)
REVERT: B  570 MET cc_start: 0.8289 (ttp) cc_final: 0.8041 (ttt)
  outliers start: 43
  outliers final: 29
  residues processed: 129
  average time/residue: 0.0988
  time to fit residues: 18.3087
Evaluate side-chains
  124 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 58 optimal weight:   50.0000
   chunk 85 optimal weight:    0.9990
   chunk 113 optimal weight:   50.0000
   chunk 76 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:   50.0000
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 HIS
** B 368 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 = 0.4361 r_free = 0.4361 target = 0.123309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.101300 restraints weight = 43399.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.103448 restraints weight = 24971.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.104917 restraints weight = 17159.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.105853 restraints weight = 13416.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.106384 restraints weight = 11465.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6606
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12122  Z= 0.118
  Angle     :  0.581  12.947  17113  Z= 0.302
  Chirality :  0.037   0.217   1990
  Planarity :  0.005   0.101   1692
  Dihedral  : 21.329 110.620   3555
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.05 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.25), residues: 1031
  helix:  0.39 (0.26), residues: 368
  sheet: -1.26 (0.42), residues: 124
  loop : -0.63 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 528 
 TYR   0.040   0.002   TYR B 547 
 PHE   0.024   0.002   PHE B 282 
 TRP   0.010   0.001   TRP A 188 
 HIS   0.005   0.001   HIS B 227 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 (12122)
  covalent geometry    : angle       0.58099 /  0.30 (17113)
  hydrogen bonds       : bond        0.04695 /  3.10 (  458)
  hydrogen bonds       : angle       5.59262 /  4.00 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.6839 (ptt180) cc_final: 0.6364 (ptp90)
REVERT: A  185 MET cc_start: 0.8678 (ptm) cc_final: 0.8430 (ptm)
REVERT: A  407 TYR cc_start: 0.7122 (m-80) cc_final: 0.6841 (m-10)
REVERT: A  529 MET cc_start: 0.8049 (ttm) cc_final: 0.7595 (tpt)
REVERT: A  570 MET cc_start: 0.7348 (ttp) cc_final: 0.6861 (tmm)
REVERT: B  148 LEU cc_start: 0.6963 (tp) cc_final: 0.6585 (tp)
REVERT: B  185 MET cc_start: 0.6562 (mmt) cc_final: 0.5852 (mmt)
REVERT: B  321 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6489 (m-80)
REVERT: B  376 ASP cc_start: 0.6575 (m-30) cc_final: 0.6200 (m-30)
REVERT: B  389 LEU cc_start: 0.8946 (tt) cc_final: 0.8440 (pp)
REVERT: B  393 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7374 (t70)
REVERT: B  399 MET cc_start: 0.6677 (tpp) cc_final: 0.6446 (tpp)
REVERT: B  529 MET cc_start: 0.7100 (tmm) cc_final: 0.6761 (tmm)
REVERT: B  570 MET cc_start: 0.8283 (ttp) cc_final: 0.7973 (ttt)
  outliers start: 43
  outliers final: 29
  residues processed: 133
  average time/residue: 0.1045
  time to fit residues: 19.2820
Evaluate side-chains
  122 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  482 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 109 optimal weight:   50.0000
   chunk 35 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    3.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 279 GLN
** B 368 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 = 0.4319 r_free = 0.4319 target = 0.120374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.098405 restraints weight = 43522.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.100512 restraints weight = 25054.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.101888 restraints weight = 17338.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.102781 restraints weight = 13618.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.103351 restraints weight = 11671.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12122  Z= 0.174
  Angle     :  0.619   9.776  17113  Z= 0.323
  Chirality :  0.039   0.221   1990
  Planarity :  0.006   0.104   1692
  Dihedral  : 21.356 113.825   3555
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 19.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.26 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.25), residues: 1031
  helix:  0.29 (0.25), residues: 371
  sheet: -1.32 (0.42), residues: 124
  loop : -0.67 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 265 
 TYR   0.032   0.002   TYR B 547 
 PHE   0.027   0.002   PHE B 418 
 TRP   0.007   0.001   TRP A 553 
 HIS   0.006   0.001   HIS B 525 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.17 (12122)
  covalent geometry    : angle       0.61859 /  0.32 (17113)
  hydrogen bonds       : bond        0.05256 /  3.50 (  458)
  hydrogen bonds       : angle       5.67862 /  4.05 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 90
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.7229 (mmp) cc_final: 0.6882 (mtt)
REVERT: A  153 ARG cc_start: 0.6718 (ptt180) cc_final: 0.6182 (ptp90)
REVERT: A  285 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7538 (tp40)
REVERT: A  399 MET cc_start: 0.6728 (mtp) cc_final: 0.6500 (mtt)
REVERT: A  407 TYR cc_start: 0.7204 (m-80) cc_final: 0.6888 (m-10)
REVERT: A  425 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7591 (p-90)
REVERT: A  529 MET cc_start: 0.8169 (ttm) cc_final: 0.7661 (tpt)
REVERT: A  570 MET cc_start: 0.7480 (ttp) cc_final: 0.6897 (tmm)
REVERT: B  185 MET cc_start: 0.6823 (mmt) cc_final: 0.5961 (mmt)
REVERT: B  321 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6237 (m-80)
REVERT: B  389 LEU cc_start: 0.9031 (tt) cc_final: 0.8442 (pp)
REVERT: B  393 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7419 (t70)
REVERT: B  398 ASN cc_start: 0.7231 (m-40) cc_final: 0.6902 (m-40)
REVERT: B  399 MET cc_start: 0.6961 (tpp) cc_final: 0.6557 (tpp)
REVERT: B  570 MET cc_start: 0.8326 (ttp) cc_final: 0.8036 (ttt)
  outliers start: 41
  outliers final: 34
  residues processed: 119
  average time/residue: 0.1005
  time to fit residues: 17.1204
Evaluate side-chains
  131 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 93
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  482 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 108 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 56 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.119307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.097187 restraints weight = 43394.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.099218 restraints weight = 25329.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.100601 restraints weight = 17633.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.101474 restraints weight = 13893.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.101926 restraints weight = 11921.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6747
moved from start:          0.4721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12122  Z= 0.176
  Angle     :  0.616   9.761  17113  Z= 0.324
  Chirality :  0.039   0.225   1990
  Planarity :  0.005   0.111   1692
  Dihedral  : 21.414 116.235   3555
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 19.93 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.25), residues: 1031
  helix:  0.28 (0.25), residues: 371
  sheet: -1.39 (0.43), residues: 124
  loop : -0.71 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 265 
 TYR   0.032   0.002   TYR B 547 
 PHE   0.021   0.003   PHE B 292 
 TRP   0.010   0.002   TRP A 188 
 HIS   0.005   0.001   HIS A 305 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 (12122)
  covalent geometry    : angle       0.61614 /  0.32 (17113)
  hydrogen bonds       : bond        0.05232 /  3.50 (  458)
  hydrogen bonds       : angle       5.65096 /  4.02 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 100
  time to evaluate  : 0.218 
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: A  107 MET cc_start: 0.7183 (mmp) cc_final: 0.6917 (mtt)
REVERT: A  153 ARG cc_start: 0.7018 (ptt180) cc_final: 0.6519 (ptp90)
REVERT: A  285 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7403 (tp40)
REVERT: A  399 MET cc_start: 0.6702 (mtp) cc_final: 0.6460 (mtt)
REVERT: A  407 TYR cc_start: 0.7206 (m-80) cc_final: 0.6898 (m-10)
REVERT: A  425 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7638 (p-90)
REVERT: A  529 MET cc_start: 0.8063 (ttm) cc_final: 0.7801 (tpt)
REVERT: A  570 MET cc_start: 0.7548 (ttp) cc_final: 0.6876 (tmm)
REVERT: B  185 MET cc_start: 0.6711 (mmt) cc_final: 0.5939 (mmt)
REVERT: B  367 ARG cc_start: 0.7037 (ttt-90) cc_final: 0.6790 (tpt-90)
REVERT: B  389 LEU cc_start: 0.9013 (tt) cc_final: 0.8473 (pp)
REVERT: B  393 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7198 (t70)
REVERT: B  398 ASN cc_start: 0.7364 (m-40) cc_final: 0.7030 (m-40)
REVERT: B  399 MET cc_start: 0.6910 (tpp) cc_final: 0.6492 (tpp)
REVERT: B  486 PHE cc_start: 0.6496 (m-80) cc_final: 0.6294 (m-80)
REVERT: B  570 MET cc_start: 0.8374 (ttp) cc_final: 0.8086 (ttt)
  outliers start: 47
  outliers final: 36
  residues processed: 134
  average time/residue: 0.0926
  time to fit residues: 17.8761
Evaluate side-chains
  133 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 94
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  157 ARG
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  494 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:   30.0000
   chunk 21 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 59 optimal weight:   50.0000
   chunk 110 optimal weight:   40.0000
   chunk 87 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.119503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.097438 restraints weight = 43378.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.099454 restraints weight = 25503.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.100833 restraints weight = 17789.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.101701 restraints weight = 14027.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.102150 restraints weight = 12055.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6726
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12122  Z= 0.157
  Angle     :  0.614   9.983  17113  Z= 0.321
  Chirality :  0.039   0.266   1990
  Planarity :  0.005   0.110   1692
  Dihedral  : 21.409 115.123   3555
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 20.93 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.25), residues: 1031
  helix:  0.28 (0.26), residues: 370
  sheet: -1.41 (0.45), residues: 117
  loop : -0.70 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 265 
 TYR   0.029   0.002   TYR B 547 
 PHE   0.034   0.003   PHE B 170 
 TRP   0.008   0.001   TRP A 553 
 HIS   0.011   0.001   HIS A 558 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 (12122)
  covalent geometry    : angle       0.61435 /  0.32 (17113)
  hydrogen bonds       : bond        0.05161 /  3.47 (  458)
  hydrogen bonds       : angle       5.62390 /  4.00 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 100
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.7087 (mmp) cc_final: 0.6878 (mtt)
REVERT: A  153 ARG cc_start: 0.6746 (ptt180) cc_final: 0.6343 (ptp90)
REVERT: A  399 MET cc_start: 0.6429 (mtp) cc_final: 0.6189 (mtt)
REVERT: A  407 TYR cc_start: 0.7072 (m-80) cc_final: 0.6835 (m-10)
REVERT: A  425 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7737 (p-90)
REVERT: A  570 MET cc_start: 0.7562 (ttp) cc_final: 0.6997 (tmm)
REVERT: B  185 MET cc_start: 0.6713 (mmt) cc_final: 0.5927 (mmt)
REVERT: B  389 LEU cc_start: 0.8975 (tt) cc_final: 0.8461 (pp)
REVERT: B  393 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7166 (t70)
REVERT: B  398 ASN cc_start: 0.7277 (m-40) cc_final: 0.6932 (m-40)
REVERT: B  399 MET cc_start: 0.6930 (tpp) cc_final: 0.6515 (tpp)
REVERT: B  513 ARG cc_start: 0.6595 (tpt90) cc_final: 0.6032 (tpt90)
REVERT: B  570 MET cc_start: 0.8387 (ttp) cc_final: 0.8089 (ttt)
  outliers start: 40
  outliers final: 34
  residues processed: 127
  average time/residue: 0.0863
  time to fit residues: 15.5124
Evaluate side-chains
  131 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  425 TRP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  482 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.120988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.099043 restraints weight = 43360.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.101116 restraints weight = 24941.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.102523 restraints weight = 17277.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.103384 restraints weight = 13623.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.103937 restraints weight = 11678.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12122  Z= 0.122
  Angle     :  0.596  10.961  17113  Z= 0.310
  Chirality :  0.038   0.253   1990
  Planarity :  0.005   0.103   1692
  Dihedral  : 21.333 113.017   3551
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.25 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.25), residues: 1031
  helix:  0.37 (0.26), residues: 365
  sheet: -1.37 (0.43), residues: 124
  loop : -0.63 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 265 
 TYR   0.029   0.002   TYR B 547 
 PHE   0.037   0.002   PHE B 170 
 TRP   0.013   0.001   TRP A 553 
 HIS   0.009   0.001   HIS A 558 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (12122)
  covalent geometry    : angle       0.59619 /  0.31 (17113)
  hydrogen bonds       : bond        0.04732 /  3.17 (  458)
  hydrogen bonds       : angle       5.48777 /  3.91 ( 1199)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.6541 (ptt180) cc_final: 0.6134 (ptp90)
REVERT: A  407 TYR cc_start: 0.7033 (m-80) cc_final: 0.6813 (m-10)
REVERT: A  517 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6922 (mp)
REVERT: A  570 MET cc_start: 0.7460 (ttp) cc_final: 0.7018 (tmm)
REVERT: B  185 MET cc_start: 0.6580 (mmt) cc_final: 0.5768 (mmt)
REVERT: B  376 ASP cc_start: 0.6280 (m-30) cc_final: 0.5966 (m-30)
REVERT: B  389 LEU cc_start: 0.8826 (tt) cc_final: 0.8319 (pp)
REVERT: B  393 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.6909 (t70)
REVERT: B  398 ASN cc_start: 0.6957 (m-40) cc_final: 0.6591 (m-40)
REVERT: B  399 MET cc_start: 0.6852 (tpp) cc_final: 0.6457 (tpp)
REVERT: B  496 MET cc_start: 0.8076 (ttm) cc_final: 0.7526 (ttp)
REVERT: B  513 ARG cc_start: 0.6262 (tpt90) cc_final: 0.5684 (tpt90)
REVERT: B  570 MET cc_start: 0.8338 (ttp) cc_final: 0.8077 (ttt)
  outliers start: 31
  outliers final: 26
  residues processed: 125
  average time/residue: 0.1011
  time to fit residues: 17.8495
Evaluate side-chains
  121 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  257 ARG
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  416 HIS
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  482 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 56 optimal weight:   30.0000
   chunk 96 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 63 optimal weight:    8.9990
   chunk 57 optimal weight:   50.0000
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 279 GLN
** B 368 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 = 0.4314 r_free = 0.4314 target = 0.120031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.098203 restraints weight = 43643.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.100231 restraints weight = 25325.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.101619 restraints weight = 17629.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.102498 restraints weight = 13911.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.103048 restraints weight = 11932.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12122  Z= 0.139
  Angle     :  0.603  11.200  17113  Z= 0.314
  Chirality :  0.038   0.253   1990
  Planarity :  0.005   0.109   1692
  Dihedral  : 21.317 114.077   3551
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.91 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.25), residues: 1031
  helix:  0.25 (0.25), residues: 366
  sheet: -1.42 (0.44), residues: 124
  loop : -0.66 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 232 
 TYR   0.027   0.002   TYR B 547 
 PHE   0.027   0.002   PHE B 170 
 TRP   0.012   0.001   TRP A 553 
 HIS   0.008   0.001   HIS B 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 (12122)
  covalent geometry    : angle       0.60279 /  0.31 (17113)
  hydrogen bonds       : bond        0.04880 /  3.27 (  458)
  hydrogen bonds       : angle       5.49813 /  3.91 ( 1199)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1791.09 seconds
wall clock time: 31 minutes 42.07 seconds (1902.07 seconds total)