Starting phenix.real_space_refine
on Wed Sep 17 18:45:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oto_13063/09_2025/7oto_13063.map"
  }
  resolution = 3.4
  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
-------------------------------------------------------------------------------
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=   0.006 sd=   0.023
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      51      5.16       5
     C    6472      2.51       5
     N    1841      2.21       5
     O    1961      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10333
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4697
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 25, 'TRANS': 576}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 711, 5572
          Classifications: {'peptide': 711}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 679}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.69, per 1000 atoms: 0.26
  Number of scatterers: 10333
  At special positions: 0
  Unit cell: (112.36, 121.9, 97.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      51     16.00
     P       6     15.00
     Mg      2     11.99
     O    1961      8.00
     N    1841      7.00
     C    6472      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: 0.99
  Conformation dependent library (CDL) restraints added in 400.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2458

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      55.3% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.720A  pdb=" N   LEU B 189 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 204
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 230 through 248
    Processing helix  chain 'B' and resid 251 through 255
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 300 through 313
    Processing helix  chain 'B' and resid 317 through 331
      removed outlier: 3.732A  pdb=" N   LEU B 321 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 346
      Proline residue:  B 340  - end of helix
      removed outlier: 3.655A  pdb=" N   GLY B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 357
    Processing helix  chain 'B' and resid 361 through 385
      Proline residue:  B 376  - end of helix
      removed outlier: 3.811A  pdb=" N   THR B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
      removed outlier: 3.578A  pdb=" N   GLY B 398 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 430 through 441
    Processing helix  chain 'B' and resid 512 through 536
    Processing helix  chain 'B' and resid 538 through 566
    Processing helix  chain 'B' and resid 585 through 592
      removed outlier: 4.078A  pdb=" N   GLN B 590 " --> pdb=" O   PRO B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 636
    Processing helix  chain 'B' and resid 668 through 684
    Processing helix  chain 'B' and resid 700 through 718
    Processing helix  chain 'B' and resid 731 through 733
      No H-bonds generated for 'chain 'B' and resid 731 through 733'
    Processing helix  chain 'B' and resid 734 through 739
      removed outlier: 4.036A  pdb=" N   LYS B 738 " --> pdb=" O   GLN B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 771 through 780
    Processing helix  chain 'B' and resid 782 through 799
    Processing helix  chain 'A' and resid 11 through 24
    Processing helix  chain 'A' and resid 41 through 52
      removed outlier: 3.617A  pdb=" N   LYS A  45 " --> pdb=" O   TYR A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 87
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 205 through 218
    Processing helix  chain 'A' and resid 230 through 249
    Processing helix  chain 'A' and resid 270 through 277
    Processing helix  chain 'A' and resid 290 through 296
    Processing helix  chain 'A' and resid 300 through 313
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 334 through 346
      Proline residue:  A 340  - end of helix
      removed outlier: 3.532A  pdb=" N   GLN A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLY A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.622A  pdb=" N   ILE A 351 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 385
      Proline residue:  A 376  - end of helix
      removed outlier: 3.525A  pdb=" N   THR A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.642A  pdb=" N   GLY A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 418 through 422
    Processing helix  chain 'A' and resid 430 through 442
    Processing helix  chain 'A' and resid 513 through 536
    Processing helix  chain 'A' and resid 538 through 566
    Processing helix  chain 'A' and resid 585 through 592
      removed outlier: 3.808A  pdb=" N   GLN A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 635
      removed outlier: 3.588A  pdb=" N   THR A 627 " --> pdb=" O   TYR A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 684
    Processing helix  chain 'A' and resid 700 through 718
    Processing helix  chain 'A' and resid 729 through 733
    Processing helix  chain 'A' and resid 734 through 739
      removed outlier: 3.624A  pdb=" N   LYS A 738 " --> pdb=" O   GLN A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 780
    Processing helix  chain 'A' and resid 782 through 800
    Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 138
      removed outlier: 3.504A  pdb=" N   ARG B 154 " --> pdb=" O   ASP B 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 178 through 181
      removed outlier: 5.894A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   TYR B 180 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 570 through 572
      removed outlier: 3.637A  pdb=" N   LYS B 644 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   GLU B 582 " --> pdb=" O   ASN B 599 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   ASN B 599 " --> pdb=" O   GLU B 582 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 653 through 656
      removed outlier: 6.222A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ASP B 693 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ARG B 656 " --> pdb=" O   ASP B 693 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B 610 " --> pdb=" O   PHE B 725 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   ALA B 749 " --> pdb=" O   THR B 613 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   SER B 761 " --> pdb=" O   ASP B 748 " (cutoff:3.500A)
      removed outlier: 8.857A  pdb=" N   LEU B 750 " --> pdb=" O   MET B 759 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   MET B 759 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 58
      removed outlier: 5.224A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A 112 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   VAL A 110 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.325A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA A 181 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   GLN A 138 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572
      removed outlier: 6.305A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS A 644 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU A 582 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   ASN A 599 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 656
      removed outlier: 6.136A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ASP A 693 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ARG A 656 " --> pdb=" O   ASP A 693 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   ASN A 744 " --> pdb=" O   GLN A 763 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   GLN A 763 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   HIS A 746 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   SER A 761 " --> pdb=" O   HIS A 746 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ASP A 748 " --> pdb=" O   MET A 759 " (cutoff:3.500A)

    568 hydrogen bonds defined for protein.
    1641 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1765
        1.31 -     1.44: 2562
        1.44 -     1.57: 6071
        1.57 -     1.69: 10
        1.69 -     1.82: 91
  Bond restraints: 10499
  Sorted by residual:
  bond pdb=" N3B ANP A1002 "
       pdb=" PG  ANP A1002 "
    ideal  model  delta    sigma   weight residual
    1.795  1.620  0.175 2.00e-02 2.50e+03 7.69e+01
  bond pdb=" N3B ANP B1002 "
       pdb=" PG  ANP B1002 "
    ideal  model  delta    sigma   weight residual
    1.795  1.631  0.164 2.00e-02 2.50e+03 6.68e+01
  bond pdb=" O3A ANP B1002 "
       pdb=" PB  ANP B1002 "
    ideal  model  delta    sigma   weight residual
    1.700  1.596  0.104 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" O3A ANP A1002 "
       pdb=" PB  ANP A1002 "
    ideal  model  delta    sigma   weight residual
    1.700  1.600  0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" N   ILE A  66 "
       pdb=" CA  ILE A  66 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 7.70e-03 1.69e+04 2.07e+01
  ... (remaining 10494 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 12438
        2.83 -     5.66: 1735
        5.66 -     8.49: 49
        8.49 -    11.32: 4
       11.32 -    14.15: 1
  Bond angle restraints: 14227
  Sorted by residual:
  angle pdb=" CA  GLY B 422 "
        pdb=" C   GLY B 422 "
        pdb=" O   GLY B 422 "
      ideal   model   delta    sigma   weight residual
     122.45  117.11    5.34 7.20e-01 1.93e+00 5.50e+01
  angle pdb=" CA  PHE A 725 "
        pdb=" CB  PHE A 725 "
        pdb=" CG  PHE A 725 "
      ideal   model   delta    sigma   weight residual
     113.80  120.50   -6.70 1.00e+00 1.00e+00 4.49e+01
  angle pdb=" N   PRO A  25 "
        pdb=" CA  PRO A  25 "
        pdb=" C   PRO A  25 "
      ideal   model   delta    sigma   weight residual
     113.40  121.99   -8.59 1.34e+00 5.57e-01 4.11e+01
  angle pdb=" CA  SER B 604 "
        pdb=" C   SER B 604 "
        pdb=" N   PRO B 605 "
      ideal   model   delta    sigma   weight residual
     117.68  122.22   -4.54 7.10e-01 1.98e+00 4.09e+01
  angle pdb=" C   PRO B 231 "
        pdb=" CA  PRO B 231 "
        pdb=" CB  PRO B 231 "
      ideal   model   delta    sigma   weight residual
     113.06  102.93   10.13 1.59e+00 3.96e-01 4.06e+01
  ... (remaining 14222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.08: 6265
       32.08 -    64.17: 176
       64.17 -    96.25: 32
       96.25 -   128.34: 1
      128.34 -   160.42: 1
  Dihedral angle restraints: 6475
    sinusoidal: 2676
      harmonic: 3799
  Sorted by residual:
  dihedral pdb=" O1A ANP B1002 "
           pdb=" O3A ANP B1002 "
           pdb=" PA  ANP B1002 "
           pdb=" PB  ANP B1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -77.31  160.42     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" O1A ANP A1002 "
           pdb=" O3A ANP A1002 "
           pdb=" PA  ANP A1002 "
           pdb=" PB  ANP A1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -39.51  122.62     1      3.00e+01 1.11e-03 1.64e+01
  dihedral pdb=" C   GLN B 248 "
           pdb=" N   GLN B 248 "
           pdb=" CA  GLN B 248 "
           pdb=" CB  GLN B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.29   -9.31     0      2.50e+00 1.60e-01 1.39e+01
  ... (remaining 6472 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 805
       0.075 -    0.149: 540
       0.149 -    0.224: 215
       0.224 -    0.299: 68
       0.299 -    0.373: 2
  Chirality restraints: 1630
  Sorted by residual:
  chirality pdb=" CB  ILE B 258 "
            pdb=" CA  ILE B 258 "
            pdb=" CG1 ILE B 258 "
            pdb=" CG2 ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" C3' ANP A1002 "
            pdb=" C2' ANP A1002 "
            pdb=" C4' ANP A1002 "
            pdb=" O3' ANP A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.72    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CA  ILE B 258 "
            pdb=" N   ILE B 258 "
            pdb=" C   ILE B 258 "
            pdb=" CB  ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1627 not shown)

  Planarity restraints: 1852
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 268 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.23e+00
        pdb=" C   ILE B 268 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ILE B 268 "    0.017 2.00e-02 2.50e+03
        pdb=" N   MET B 269 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 675 "   -0.011 2.00e-02 2.50e+03   2.35e-02 5.51e+00
        pdb=" C   THR B 675 "    0.041 2.00e-02 2.50e+03
        pdb=" O   THR B 675 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU B 676 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 213 "   -0.011 2.00e-02 2.50e+03   2.32e-02 5.38e+00
        pdb=" C   LEU B 213 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LEU B 213 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN B 214 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1849 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 4
        2.42 -     3.04: 5531
        3.04 -     3.66: 15957
        3.66 -     4.28: 22989
        4.28 -     4.90: 39179
  Nonbonded interactions: 83660
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 621 "
            pdb="MG    MG A1001 "
     model   vdw
     1.799 2.170
  nonbonded pdb=" OG  SER B 621 "
            pdb="MG    MG B1001 "
     model   vdw
     2.036 2.170
  nonbonded pdb="MG    MG A1001 "
            pdb=" O2B ANP A1002 "
     model   vdw
     2.128 2.170
  nonbonded pdb="MG    MG B1001 "
            pdb=" O1G ANP B1002 "
     model   vdw
     2.273 2.170
  nonbonded pdb=" N   ASP A 139 "
            pdb=" O   ASP A 139 "
     model   vdw
     2.439 2.496
  ... (remaining 83655 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.130
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.720
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
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      :  0.013   0.175  10499  Z= 0.975
  Angle     :  1.836  14.147  14227  Z= 1.411
  Chirality :  0.110   0.373   1630
  Planarity :  0.006   0.034   1852
  Dihedral  : 15.716 160.421   4017
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.21), residues: 1301
  helix:  3.35 (0.17), residues: 662
  sheet:  0.72 (0.39), residues: 159
  loop : -0.34 (0.24), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 607 
 TYR   0.035   0.003   TYR A  31 
 PHE   0.029   0.005   PHE B 532 
 TRP   0.020   0.003   TRP B 202 
 HIS   0.010   0.002   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.01297 (10499)
  covalent geometry    : angle       1.83605 (14227)
  hydrogen bonds       : bond        0.20863 (  568)
  hydrogen bonds       : angle       6.18931 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 359
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 THR cc_start: 0.8305 (t) cc_final: 0.8057 (m)
REVERT: B  197 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7336 (mtp180)
REVERT: B  198 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7546 (mtm-85)
REVERT: B  201 LEU cc_start: 0.8205 (tp) cc_final: 0.7935 (mm)
REVERT: B  205 GLU cc_start: 0.7437 (tt0) cc_final: 0.7155 (tt0)
REVERT: B  229 ASN cc_start: 0.7428 (t0) cc_final: 0.7009 (p0)
REVERT: B  323 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7516 (mt-10)
REVERT: B  355 LEU cc_start: 0.7836 (tp) cc_final: 0.7580 (tp)
REVERT: B  373 GLN cc_start: 0.7608 (mt0) cc_final: 0.7377 (mm110)
REVERT: B  386 ASP cc_start: 0.7722 (p0) cc_final: 0.7381 (p0)
REVERT: B  402 GLU cc_start: 0.7532 (tp30) cc_final: 0.7264 (tp30)
REVERT: B  535 LEU cc_start: 0.7229 (mt) cc_final: 0.6904 (mp)
REVERT: B  566 ASN cc_start: 0.8095 (t0) cc_final: 0.7667 (t0)
REVERT: B  640 VAL cc_start: 0.8618 (t) cc_final: 0.8350 (m)
REVERT: B  656 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6414 (tpt90)
REVERT: B  692 MET cc_start: 0.8587 (mtp) cc_final: 0.8342 (mtt)
REVERT: B  693 ASP cc_start: 0.8164 (t0) cc_final: 0.7802 (t0)
REVERT: B  718 LYS cc_start: 0.8163 (mttm) cc_final: 0.7925 (ttmm)
REVERT: A   52 ASP cc_start: 0.8157 (t0) cc_final: 0.7738 (t0)
REVERT: A   96 ILE cc_start: 0.6907 (pt) cc_final: 0.6607 (mm)
REVERT: A  122 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7628 (tp30)
REVERT: A  130 ASP cc_start: 0.8327 (m-30) cc_final: 0.8018 (p0)
REVERT: A  162 ASP cc_start: 0.7343 (m-30) cc_final: 0.6791 (t0)
REVERT: A  166 MET cc_start: 0.7816 (tpt) cc_final: 0.7584 (tpp)
REVERT: A  198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7853 (ttm-80)
REVERT: A  225 PHE cc_start: 0.7779 (m-80) cc_final: 0.7426 (m-80)
REVERT: A  240 LEU cc_start: 0.8064 (tp) cc_final: 0.7734 (tp)
REVERT: A  283 LEU cc_start: 0.7896 (mt) cc_final: 0.7661 (mp)
REVERT: A  296 ASP cc_start: 0.7792 (t0) cc_final: 0.7486 (t0)
REVERT: A  355 LEU cc_start: 0.7303 (tp) cc_final: 0.6766 (tp)
REVERT: A  417 VAL cc_start: 0.7812 (t) cc_final: 0.7495 (m)
REVERT: A  566 ASN cc_start: 0.8189 (t0) cc_final: 0.7639 (t0)
REVERT: A  651 ASP cc_start: 0.8132 (t70) cc_final: 0.7869 (t0)
REVERT: A  661 ASP cc_start: 0.7631 (t0) cc_final: 0.7427 (t0)
REVERT: A  662 ASP cc_start: 0.6550 (t0) cc_final: 0.6103 (p0)
REVERT: A  667 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7258 (mmm-85)
REVERT: A  692 MET cc_start: 0.8278 (mtm) cc_final: 0.8015 (mtp)
REVERT: A  713 GLU cc_start: 0.7284 (tt0) cc_final: 0.7077 (tt0)
REVERT: A  720 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7509 (mtmm)
REVERT: A  759 MET cc_start: 0.8355 (mmm) cc_final: 0.8075 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 359
  average time/residue: 0.1616
  time to fit residues: 73.6689
Evaluate side-chains
  292 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 538 HIS
B 734 GLN
B 746 HIS
A  49 GLN
A  78 ASN
A 254 HIS
A 264 GLN
A 543 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.120379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113818 restraints weight = 19426.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.32
r_work: 0.3336 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10499  Z= 0.147
  Angle     :  0.598   7.159  14227  Z= 0.318
  Chirality :  0.041   0.177   1630
  Planarity :  0.005   0.041   1852
  Dihedral  :  8.691 166.207   1511
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.75 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.22), residues: 1301
  helix:  2.97 (0.19), residues: 677
  sheet:  0.71 (0.37), residues: 184
  loop : -0.65 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 319 
 TYR   0.022   0.002   TYR A  31 
 PHE   0.017   0.002   PHE A 725 
 TRP   0.012   0.002   TRP A 137 
 HIS   0.009   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10499)
  covalent geometry    : angle       0.59766 (14227)
  hydrogen bonds       : bond        0.05185 (  568)
  hydrogen bonds       : angle       4.63559 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 293
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8483 (tp) cc_final: 0.8281 (mm)
REVERT: B  229 ASN cc_start: 0.7282 (t0) cc_final: 0.6878 (p0)
REVERT: B  302 MET cc_start: 0.7506 (ptm) cc_final: 0.7221 (ptt)
REVERT: B  350 ARG cc_start: 0.6392 (ptt-90) cc_final: 0.5775 (ttp80)
REVERT: B  354 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7559 (mtt180)
REVERT: B  355 LEU cc_start: 0.8855 (tp) cc_final: 0.8565 (tp)
REVERT: B  386 ASP cc_start: 0.7154 (p0) cc_final: 0.6763 (p0)
REVERT: B  424 VAL cc_start: 0.8650 (t) cc_final: 0.8326 (p)
REVERT: B  566 ASN cc_start: 0.8083 (t0) cc_final: 0.7755 (t0)
REVERT: B  624 MET cc_start: 0.8431 (mtp) cc_final: 0.8172 (mtp)
REVERT: B  640 VAL cc_start: 0.8804 (t) cc_final: 0.8413 (m)
REVERT: B  667 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7294 (mtm-85)
REVERT: B  692 MET cc_start: 0.8429 (mtp) cc_final: 0.8190 (mtt)
REVERT: B  693 ASP cc_start: 0.7752 (t0) cc_final: 0.7532 (t70)
REVERT: A   36 PHE cc_start: 0.7839 (m-10) cc_final: 0.7567 (m-10)
REVERT: A  133 LEU cc_start: 0.8393 (tp) cc_final: 0.8169 (tp)
REVERT: A  157 LEU cc_start: 0.8161 (tt) cc_final: 0.7675 (tp)
REVERT: A  198 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.8004 (ttm-80)
REVERT: A  199 ARG cc_start: 0.8311 (mmm160) cc_final: 0.8091 (mmm160)
REVERT: A  240 LEU cc_start: 0.8387 (tp) cc_final: 0.8027 (tp)
REVERT: A  296 ASP cc_start: 0.7783 (t0) cc_final: 0.7395 (t0)
REVERT: A  355 LEU cc_start: 0.7716 (tp) cc_final: 0.7204 (tp)
REVERT: A  417 VAL cc_start: 0.7403 (t) cc_final: 0.7148 (p)
REVERT: A  532 PHE cc_start: 0.8063 (m-80) cc_final: 0.7858 (m-10)
REVERT: A  565 LEU cc_start: 0.8309 (mt) cc_final: 0.7796 (mt)
REVERT: A  566 ASN cc_start: 0.8123 (t0) cc_final: 0.7453 (t0)
REVERT: A  590 GLN cc_start: 0.7800 (tp40) cc_final: 0.7577 (tp40)
REVERT: A  692 MET cc_start: 0.8115 (mtm) cc_final: 0.7820 (mtp)
  outliers start: 25
  outliers final: 12
  residues processed: 305
  average time/residue: 0.1423
  time to fit residues: 56.8708
Evaluate side-chains
  270 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 258
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  695 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 124 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 602 ASN
B 734 GLN
A 248 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.114262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107949 restraints weight = 19663.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.29
r_work: 0.3213 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  10499  Z= 0.271
  Angle     :  0.701   9.805  14227  Z= 0.361
  Chirality :  0.047   0.242   1630
  Planarity :  0.006   0.075   1852
  Dihedral  :  7.783 158.695   1511
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.51 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.22), residues: 1301
  helix:  2.16 (0.19), residues: 666
  sheet:  0.54 (0.39), residues: 173
  loop : -0.95 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 579 
 TYR   0.025   0.002   TYR A 635 
 PHE   0.020   0.003   PHE A  30 
 TRP   0.019   0.003   TRP A 137 
 HIS   0.010   0.003   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00664 (10499)
  covalent geometry    : angle       0.70065 (14227)
  hydrogen bonds       : bond        0.05943 (  568)
  hydrogen bonds       : angle       4.63998 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 273
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8785 (tp) cc_final: 0.8414 (mm)
REVERT: B  229 ASN cc_start: 0.7317 (t0) cc_final: 0.6898 (p0)
REVERT: B  354 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7614 (mtt180)
REVERT: B  373 GLN cc_start: 0.7877 (mm110) cc_final: 0.7549 (mm-40)
REVERT: B  386 ASP cc_start: 0.7106 (p0) cc_final: 0.6602 (p0)
REVERT: B  560 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: B  640 VAL cc_start: 0.8845 (t) cc_final: 0.8556 (m)
REVERT: B  693 ASP cc_start: 0.7860 (t0) cc_final: 0.7575 (t70)
REVERT: B  734 GLN cc_start: 0.8202 (mt0) cc_final: 0.7882 (mt0)
REVERT: B  784 GLU cc_start: 0.7269 (tp30) cc_final: 0.7022 (tp30)
REVERT: A  182 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7177 (pt0)
REVERT: A  198 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8081 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7935 (tp) cc_final: 0.7443 (tp)
REVERT: A  412 ILE cc_start: 0.8347 (pt) cc_final: 0.8135 (pt)
REVERT: A  417 VAL cc_start: 0.7540 (t) cc_final: 0.7296 (p)
REVERT: A  566 ASN cc_start: 0.8104 (t0) cc_final: 0.7469 (t0)
REVERT: A  692 MET cc_start: 0.8118 (mtm) cc_final: 0.7875 (mtp)
REVERT: A  739 MET cc_start: 0.7271 (ttm) cc_final: 0.6976 (ptp)
  outliers start: 41
  outliers final: 27
  residues processed: 291
  average time/residue: 0.1467
  time to fit residues: 55.5284
Evaluate side-chains
  280 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 252
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  625 ARG
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 127 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 117 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.115194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108559 restraints weight = 19534.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.37
r_work: 0.3234 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  10499  Z= 0.195
  Angle     :  0.612  10.800  14227  Z= 0.315
  Chirality :  0.042   0.148   1630
  Planarity :  0.005   0.062   1852
  Dihedral  :  7.475 160.775   1511
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.17 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.22), residues: 1301
  helix:  2.20 (0.19), residues: 662
  sheet:  0.24 (0.38), residues: 180
  loop : -1.06 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 667 
 TYR   0.018   0.002   TYR A  31 
 PHE   0.026   0.002   PHE A  36 
 TRP   0.016   0.002   TRP A 137 
 HIS   0.006   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10499)
  covalent geometry    : angle       0.61218 (14227)
  hydrogen bonds       : bond        0.04888 (  568)
  hydrogen bonds       : angle       4.45469 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 262
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  156 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7977 (mtt180)
REVERT: B  201 LEU cc_start: 0.8891 (tp) cc_final: 0.8487 (tp)
REVERT: B  205 GLU cc_start: 0.7030 (mp0) cc_final: 0.6623 (mp0)
REVERT: B  229 ASN cc_start: 0.7352 (t0) cc_final: 0.6877 (p0)
REVERT: B  302 MET cc_start: 0.7637 (ptm) cc_final: 0.7349 (ptt)
REVERT: B  350 ARG cc_start: 0.6814 (ttp-110) cc_final: 0.6131 (ttp80)
REVERT: B  560 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: B  565 LEU cc_start: 0.8286 (mt) cc_final: 0.8083 (mt)
REVERT: B  640 VAL cc_start: 0.8848 (t) cc_final: 0.8510 (m)
REVERT: B  693 ASP cc_start: 0.7870 (t0) cc_final: 0.7622 (t0)
REVERT: B  738 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8135 (mtmm)
REVERT: B  784 GLU cc_start: 0.7191 (tp30) cc_final: 0.6941 (tp30)
REVERT: A   82 LYS cc_start: 0.8459 (mttm) cc_final: 0.8169 (mttt)
REVERT: A  171 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: A  182 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7137 (pt0)
REVERT: A  198 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.7906 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7799 (tp) cc_final: 0.7354 (tp)
REVERT: A  412 ILE cc_start: 0.8219 (pt) cc_final: 0.8003 (pt)
REVERT: A  414 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (p)
REVERT: A  417 VAL cc_start: 0.7587 (t) cc_final: 0.7323 (p)
REVERT: A  566 ASN cc_start: 0.8178 (t0) cc_final: 0.7473 (t0)
REVERT: A  575 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7450 (ttmm)
REVERT: A  692 MET cc_start: 0.8132 (mtm) cc_final: 0.7866 (mtp)
  outliers start: 37
  outliers final: 25
  residues processed: 283
  average time/residue: 0.1356
  time to fit residues: 50.3880
Evaluate side-chains
  278 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 251
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 96 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0670
   chunk 82 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   overall best weight:    3.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 248 GLN
A 381 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.114706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108237 restraints weight = 19609.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.32
r_work: 0.3230 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10499  Z= 0.181
  Angle     :  0.595  10.147  14227  Z= 0.305
  Chirality :  0.041   0.149   1630
  Planarity :  0.005   0.065   1852
  Dihedral  :  7.380 159.271   1511
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.00 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.37 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.22), residues: 1301
  helix:  2.21 (0.19), residues: 661
  sheet:  0.20 (0.38), residues: 180
  loop : -1.03 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 667 
 TYR   0.019   0.002   TYR A  31 
 PHE   0.014   0.002   PHE A  30 
 TRP   0.015   0.002   TRP A 137 
 HIS   0.009   0.002   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (10499)
  covalent geometry    : angle       0.59522 (14227)
  hydrogen bonds       : bond        0.04740 (  568)
  hydrogen bonds       : angle       4.38913 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 261
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7389 (ttm-80)
REVERT: B  156 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7611 (mtt180)
REVERT: B  201 LEU cc_start: 0.8907 (tp) cc_final: 0.8703 (tp)
REVERT: B  205 GLU cc_start: 0.7039 (mp0) cc_final: 0.6721 (mp0)
REVERT: B  229 ASN cc_start: 0.7364 (t0) cc_final: 0.6887 (p0)
REVERT: B  302 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7320 (ptt)
REVERT: B  350 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6603 (ttp80)
REVERT: B  373 GLN cc_start: 0.7884 (mm110) cc_final: 0.7556 (mm-40)
REVERT: B  393 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7673 (mp)
REVERT: B  560 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: B  640 VAL cc_start: 0.8848 (t) cc_final: 0.8494 (m)
REVERT: B  667 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7556 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7825 (t0) cc_final: 0.7586 (t0)
REVERT: B  695 ILE cc_start: 0.8377 (tt) cc_final: 0.8146 (mm)
REVERT: B  738 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8127 (mtmm)
REVERT: B  784 GLU cc_start: 0.7165 (tp30) cc_final: 0.6908 (tp30)
REVERT: A   82 LYS cc_start: 0.8478 (mttm) cc_final: 0.8209 (mttt)
REVERT: A  166 MET cc_start: 0.7999 (tpp) cc_final: 0.7549 (tpp)
REVERT: A  171 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: A  182 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7170 (pt0)
REVERT: A  198 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8130 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7718 (tp) cc_final: 0.7323 (tp)
REVERT: A  412 ILE cc_start: 0.8207 (pt) cc_final: 0.7979 (pt)
REVERT: A  417 VAL cc_start: 0.7599 (t) cc_final: 0.7350 (p)
REVERT: A  566 ASN cc_start: 0.8160 (t0) cc_final: 0.7474 (t0)
REVERT: A  575 LYS cc_start: 0.7623 (mtmm) cc_final: 0.7404 (ttmm)
REVERT: A  692 MET cc_start: 0.8125 (mtm) cc_final: 0.7856 (mtp)
  outliers start: 39
  outliers final: 26
  residues processed: 283
  average time/residue: 0.1439
  time to fit residues: 53.0241
Evaluate side-chains
  285 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 256
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 128 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0050
   chunk 55 optimal weight:    0.9990
   chunk 120 optimal weight:    7.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
A 590 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111130 restraints weight = 19847.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.33
r_work: 0.3255 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10499  Z= 0.146
  Angle     :  0.566   9.207  14227  Z= 0.290
  Chirality :  0.040   0.137   1630
  Planarity :  0.005   0.071   1852
  Dihedral  :  7.248 159.179   1511
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.77 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.90 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.23), residues: 1301
  helix:  2.37 (0.20), residues: 658
  sheet:  0.15 (0.38), residues: 180
  loop : -0.95 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 220 
 TYR   0.017   0.001   TYR A  31 
 PHE   0.011   0.001   PHE A  36 
 TRP   0.012   0.002   TRP A 137 
 HIS   0.006   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10499)
  covalent geometry    : angle       0.56650 (14227)
  hydrogen bonds       : bond        0.04268 (  568)
  hydrogen bonds       : angle       4.27232 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7514 (ttm-80)
REVERT: B  156 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7703 (mmt180)
REVERT: B  205 GLU cc_start: 0.7025 (mp0) cc_final: 0.6718 (mp0)
REVERT: B  229 ASN cc_start: 0.7367 (t0) cc_final: 0.6983 (p0)
REVERT: B  302 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7250 (ptt)
REVERT: B  350 ARG cc_start: 0.6779 (ttp-110) cc_final: 0.6481 (ttp80)
REVERT: B  354 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7294 (mtt180)
REVERT: B  560 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7357 (tm-30)
REVERT: B  640 VAL cc_start: 0.8837 (t) cc_final: 0.8474 (m)
REVERT: B  667 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7471 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7822 (t0) cc_final: 0.7588 (t0)
REVERT: B  784 GLU cc_start: 0.7150 (tp30) cc_final: 0.6900 (tp30)
REVERT: A   82 LYS cc_start: 0.8379 (mttm) cc_final: 0.8072 (mtmt)
REVERT: A  166 MET cc_start: 0.7956 (tpp) cc_final: 0.7655 (tpp)
REVERT: A  198 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8109 (ttm-80)
REVERT: A  351 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (mt)
REVERT: A  355 LEU cc_start: 0.7640 (tp) cc_final: 0.7272 (tp)
REVERT: A  412 ILE cc_start: 0.8137 (pt) cc_final: 0.7909 (pt)
REVERT: A  417 VAL cc_start: 0.7621 (t) cc_final: 0.7369 (p)
REVERT: A  566 ASN cc_start: 0.8122 (t0) cc_final: 0.7497 (t0)
REVERT: A  692 MET cc_start: 0.8195 (mtm) cc_final: 0.7929 (mtp)
  outliers start: 42
  outliers final: 29
  residues processed: 288
  average time/residue: 0.1425
  time to fit residues: 53.5134
Evaluate side-chains
  291 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 260
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  590 GLN
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 112 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
A 590 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.117664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.111194 restraints weight = 19504.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.33
r_work: 0.3234 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10499  Z= 0.167
  Angle     :  0.583   9.538  14227  Z= 0.298
  Chirality :  0.040   0.138   1630
  Planarity :  0.005   0.073   1852
  Dihedral  :  7.225 158.495   1511
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.08 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.82 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.23), residues: 1301
  helix:  2.34 (0.20), residues: 657
  sheet: -0.02 (0.37), residues: 195
  loop : -0.93 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 579 
 TYR   0.018   0.002   TYR A  31 
 PHE   0.012   0.002   PHE A  36 
 TRP   0.013   0.002   TRP A 137 
 HIS   0.005   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (10499)
  covalent geometry    : angle       0.58281 (14227)
  hydrogen bonds       : bond        0.04349 (  568)
  hydrogen bonds       : angle       4.25676 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 264
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7393 (ttm-80)
REVERT: B  205 GLU cc_start: 0.7050 (mp0) cc_final: 0.6777 (mp0)
REVERT: B  229 ASN cc_start: 0.7447 (t0) cc_final: 0.7078 (p0)
REVERT: B  302 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7282 (ptt)
REVERT: B  350 ARG cc_start: 0.6911 (ttp-110) cc_final: 0.6304 (ttp80)
REVERT: B  354 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7304 (mtt180)
REVERT: B  373 GLN cc_start: 0.7903 (mm110) cc_final: 0.7535 (mm-40)
REVERT: B  393 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7689 (mp)
REVERT: B  560 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: B  640 VAL cc_start: 0.8831 (t) cc_final: 0.8468 (m)
REVERT: B  667 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7521 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7833 (t0) cc_final: 0.7595 (t0)
REVERT: B  738 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8170 (mtmm)
REVERT: B  784 GLU cc_start: 0.7182 (tp30) cc_final: 0.6912 (tp30)
REVERT: A   82 LYS cc_start: 0.8374 (mttm) cc_final: 0.8093 (mtmt)
REVERT: A  166 MET cc_start: 0.7963 (tpp) cc_final: 0.7586 (tpp)
REVERT: A  198 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.8077 (ttm-80)
REVERT: A  199 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8164 (mmm160)
REVERT: A  355 LEU cc_start: 0.7655 (tp) cc_final: 0.7306 (tp)
REVERT: A  412 ILE cc_start: 0.8160 (pt) cc_final: 0.7958 (pt)
REVERT: A  417 VAL cc_start: 0.7673 (t) cc_final: 0.7445 (p)
REVERT: A  566 ASN cc_start: 0.8105 (t0) cc_final: 0.7551 (t0)
REVERT: A  692 MET cc_start: 0.8196 (mtm) cc_final: 0.7914 (mtp)
  outliers start: 36
  outliers final: 29
  residues processed: 284
  average time/residue: 0.1470
  time to fit residues: 53.9516
Evaluate side-chains
  295 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  786 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 116 optimal weight:    8.9990
   chunk 127 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108668 restraints weight = 19703.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.32
r_work: 0.3234 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10499  Z= 0.181
  Angle     :  0.600   9.465  14227  Z= 0.306
  Chirality :  0.041   0.144   1630
  Planarity :  0.005   0.069   1852
  Dihedral  :  7.237 157.723   1511
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.15 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.10 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.23), residues: 1301
  helix:  2.26 (0.20), residues: 658
  sheet: -0.05 (0.37), residues: 194
  loop : -0.95 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 667 
 TYR   0.017   0.002   TYR A  31 
 PHE   0.013   0.002   PHE A  30 
 TRP   0.014   0.002   TRP A 137 
 HIS   0.006   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10499)
  covalent geometry    : angle       0.60008 (14227)
  hydrogen bonds       : bond        0.04514 (  568)
  hydrogen bonds       : angle       4.30175 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 267
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7359 (ttm-80)
REVERT: B  205 GLU cc_start: 0.7064 (mp0) cc_final: 0.6803 (mp0)
REVERT: B  229 ASN cc_start: 0.7332 (t0) cc_final: 0.7022 (p0)
REVERT: B  302 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (ptt)
REVERT: B  350 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6261 (ttp80)
REVERT: B  354 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7257 (mtt180)
REVERT: B  373 GLN cc_start: 0.7890 (mm110) cc_final: 0.7557 (mm-40)
REVERT: B  393 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: B  560 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7404 (tm-30)
REVERT: B  635 TYR cc_start: 0.8371 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  640 VAL cc_start: 0.8732 (t) cc_final: 0.8382 (m)
REVERT: B  656 ARG cc_start: 0.7439 (tpt90) cc_final: 0.6913 (tpt90)
REVERT: B  667 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7590 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7865 (t0) cc_final: 0.7618 (t0)
REVERT: B  738 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8198 (mtmm)
REVERT: B  784 GLU cc_start: 0.7178 (tp30) cc_final: 0.6919 (tp30)
REVERT: A   82 LYS cc_start: 0.8423 (mttm) cc_final: 0.8172 (mtmt)
REVERT: A  166 MET cc_start: 0.7939 (tpp) cc_final: 0.7610 (tpp)
REVERT: A  198 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8090 (ttm-80)
REVERT: A  351 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (mt)
REVERT: A  355 LEU cc_start: 0.7649 (tp) cc_final: 0.7300 (tp)
REVERT: A  412 ILE cc_start: 0.8213 (pt) cc_final: 0.8003 (pt)
REVERT: A  417 VAL cc_start: 0.7717 (t) cc_final: 0.7482 (p)
REVERT: A  566 ASN cc_start: 0.8086 (t0) cc_final: 0.7499 (t0)
REVERT: A  575 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7358 (ttmm)
REVERT: A  692 MET cc_start: 0.8223 (mtm) cc_final: 0.7941 (mtp)
  outliers start: 37
  outliers final: 29
  residues processed: 288
  average time/residue: 0.1435
  time to fit residues: 53.7762
Evaluate side-chains
  292 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  786 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 127 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 129 optimal weight:    0.4980
   chunk 120 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 254 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.120209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.113651 restraints weight = 19449.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.37
r_work: 0.3284 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10499  Z= 0.113
  Angle     :  0.558   8.027  14227  Z= 0.285
  Chirality :  0.038   0.132   1630
  Planarity :  0.004   0.059   1852
  Dihedral  :  7.061 158.758   1511
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.92 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.93 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.23), residues: 1301
  helix:  2.59 (0.20), residues: 660
  sheet: -0.00 (0.37), residues: 196
  loop : -0.87 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 220 
 TYR   0.016   0.001   TYR A  31 
 PHE   0.028   0.001   PHE A 334 
 TRP   0.009   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10499)
  covalent geometry    : angle       0.55757 (14227)
  hydrogen bonds       : bond        0.03498 (  568)
  hydrogen bonds       : angle       4.12509 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 265
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7406 (ttm-80)
REVERT: B  205 GLU cc_start: 0.7011 (mp0) cc_final: 0.6763 (mp0)
REVERT: B  229 ASN cc_start: 0.7344 (t0) cc_final: 0.6979 (p0)
REVERT: B  302 MET cc_start: 0.7355 (ptm) cc_final: 0.7119 (ptt)
REVERT: B  350 ARG cc_start: 0.6811 (ttp-110) cc_final: 0.6148 (ttp80)
REVERT: B  354 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7491 (mtt180)
REVERT: B  373 GLN cc_start: 0.7887 (mm110) cc_final: 0.7537 (mm-40)
REVERT: B  560 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: B  640 VAL cc_start: 0.8797 (t) cc_final: 0.8458 (m)
REVERT: B  656 ARG cc_start: 0.7437 (tpt90) cc_final: 0.6938 (tpt90)
REVERT: B  667 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7557 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7828 (t0) cc_final: 0.7598 (t0)
REVERT: B  784 GLU cc_start: 0.7081 (tp30) cc_final: 0.6868 (tp30)
REVERT: A  198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8029 (ttm-80)
REVERT: A  199 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8091 (mmm160)
REVERT: A  219 THR cc_start: 0.8635 (m) cc_final: 0.8351 (p)
REVERT: A  351 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: A  355 LEU cc_start: 0.7523 (tp) cc_final: 0.7184 (tp)
REVERT: A  417 VAL cc_start: 0.7759 (t) cc_final: 0.7547 (p)
REVERT: A  566 ASN cc_start: 0.8018 (t0) cc_final: 0.7512 (t0)
REVERT: A  667 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7770 (mtp85)
REVERT: A  692 MET cc_start: 0.8197 (mtm) cc_final: 0.7907 (mtp)
REVERT: A  695 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7985 (pt)
  outliers start: 30
  outliers final: 21
  residues processed: 282
  average time/residue: 0.1437
  time to fit residues: 52.9893
Evaluate side-chains
  289 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 266
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  756 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 124 optimal weight:    0.0870
   chunk 36 optimal weight:    0.5980
   chunk 52 optimal weight:    0.4980
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 100 optimal weight:    0.0970
   chunk 53 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
B 212 GLN
B 744 ASN
A 254 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.120217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113888 restraints weight = 19320.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.33
r_work: 0.3295 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10499  Z= 0.112
  Angle     :  0.573   9.158  14227  Z= 0.292
  Chirality :  0.038   0.136   1630
  Planarity :  0.004   0.054   1852
  Dihedral  :  6.961 157.883   1511
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.00 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.94 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.23), residues: 1301
  helix:  2.68 (0.20), residues: 661
  sheet:  0.08 (0.38), residues: 191
  loop : -0.84 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 220 
 TYR   0.015   0.001   TYR A  31 
 PHE   0.038   0.001   PHE A 334 
 TRP   0.009   0.001   TRP B 709 
 HIS   0.006   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10499)
  covalent geometry    : angle       0.57307 (14227)
  hydrogen bonds       : bond        0.03327 (  568)
  hydrogen bonds       : angle       4.07191 ( 1641)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 270
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7413 (ttm-80)
REVERT: B  205 GLU cc_start: 0.7033 (mp0) cc_final: 0.6791 (mp0)
REVERT: B  229 ASN cc_start: 0.7237 (t0) cc_final: 0.6963 (p0)
REVERT: B  302 MET cc_start: 0.7331 (ptm) cc_final: 0.7073 (ptt)
REVERT: B  350 ARG cc_start: 0.6808 (ttp-110) cc_final: 0.6122 (ttp80)
REVERT: B  354 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7468 (mtt180)
REVERT: B  560 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: B  566 ASN cc_start: 0.8174 (t0) cc_final: 0.7864 (t0)
REVERT: B  635 TYR cc_start: 0.8073 (m-80) cc_final: 0.7661 (m-80)
REVERT: B  640 VAL cc_start: 0.8757 (t) cc_final: 0.8432 (m)
REVERT: B  656 ARG cc_start: 0.7399 (tpt90) cc_final: 0.6934 (tpt90)
REVERT: B  667 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7422 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7762 (t0) cc_final: 0.7562 (t70)
REVERT: A   33 MET cc_start: 0.7581 (mmm) cc_final: 0.7244 (mmm)
REVERT: A  198 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7984 (ttm-80)
REVERT: A  199 ARG cc_start: 0.8342 (mmm160) cc_final: 0.8053 (mmm160)
REVERT: A  219 THR cc_start: 0.8672 (m) cc_final: 0.8361 (p)
REVERT: A  351 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7804 (mm)
REVERT: A  355 LEU cc_start: 0.7505 (tp) cc_final: 0.7173 (tp)
REVERT: A  566 ASN cc_start: 0.7987 (t0) cc_final: 0.7531 (t0)
REVERT: A  626 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8210 (pt0)
REVERT: A  692 MET cc_start: 0.8171 (mtm) cc_final: 0.7867 (mtp)
REVERT: A  695 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7939 (pt)
REVERT: A  763 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7946 (mm-40)
  outliers start: 21
  outliers final: 17
  residues processed: 283
  average time/residue: 0.1487
  time to fit residues: 54.5791
Evaluate side-chains
  283 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 263
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
B 373 GLN
B 744 ASN
A 254 HIS
A 717 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110772 restraints weight = 19702.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.35
r_work: 0.3233 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  10499  Z= 0.225
  Angle     :  0.660   9.369  14227  Z= 0.337
  Chirality :  0.043   0.179   1630
  Planarity :  0.005   0.053   1852
  Dihedral  :  7.217 156.366   1511
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.23 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.85 %
    Favored  : 76.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.23), residues: 1301
  helix:  2.29 (0.20), residues: 659
  sheet: -0.05 (0.37), residues: 193
  loop : -0.91 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 163 
 TYR   0.019   0.002   TYR A 635 
 PHE   0.016   0.002   PHE A  30 
 TRP   0.015   0.002   TRP A 137 
 HIS   0.008   0.002   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 (10499)
  covalent geometry    : angle       0.66002 (14227)
  hydrogen bonds       : bond        0.04614 (  568)
  hydrogen bonds       : angle       4.26676 ( 1641)

===============================================================================
Job complete
usr+sys time: 2461.44 seconds
wall clock time: 42 minutes 51.12 seconds (2571.12 seconds total)