Starting phenix.real_space_refine
on Fri Feb 14 18:46:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oto_13063/02_2025/7oto_13063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oto_13063/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oto_13063/02_2025/7oto_13063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oto_13063/02_2025/7oto_13063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oto_13063/02_2025/7oto_13063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oto_13063/02_2025/7oto_13063.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.23, per 1000 atoms: 0.60
  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: 2.63
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.14
  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: 3.82

  Time building geometry restraints manager: 3.10 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:             0.080
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.300
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.980
-------------------------------------------------------------------------------
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= 0.833
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.020   0.003   TRP B 202 
 HIS   0.010   0.002   HIS B 752 
 PHE   0.029   0.005   PHE B 532 
 TYR   0.035   0.003   TYR A  31 
 ARG   0.007   0.001   ARG B 607 

*********************** 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  : 1.145 
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: 0.7328 (mtp180)
REVERT: B  198 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7511 (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  242 GLN cc_start: 0.7209 (tp40) cc_final: 0.6973 (tm-30)
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: 0.6903 (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: 0.7076 (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: 0.3402
  time to fit residues: 155.4324
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  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 99 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.119765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.113050 restraints weight = 19172.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.36
r_work: 0.3310 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10499  Z= 0.242
  Angle     :  0.619   7.376  14227  Z= 0.327
  Chirality :  0.043   0.188   1630
  Planarity :  0.005   0.040   1852
  Dihedral  :  8.694 166.265   1511
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.75 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.22), residues: 1301
  helix:  2.83 (0.19), residues: 676
  sheet:  0.69 (0.37), residues: 185
  loop : -0.71 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 137 
 HIS   0.009   0.002   HIS A  74 
 PHE   0.017   0.002   PHE A  36 
 TYR   0.021   0.002   TYR A  31 
 ARG   0.009   0.001   ARG B 199 

*********************** 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
  320 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 294
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8610 (tp) cc_final: 0.8409 (mm)
REVERT: B  229 ASN cc_start: 0.7342 (t0) cc_final: 0.6962 (p0)
REVERT: B  302 MET cc_start: 0.7567 (ptm) cc_final: 0.7308 (ptt)
REVERT: B  354 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7798 (mtt180)
REVERT: B  355 LEU cc_start: 0.8886 (tp) cc_final: 0.8594 (tp)
REVERT: B  363 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7675 (mtt180)
REVERT: B  424 VAL cc_start: 0.8688 (t) cc_final: 0.8365 (p)
REVERT: B  566 ASN cc_start: 0.8127 (t0) cc_final: 0.7777 (t0)
REVERT: B  624 MET cc_start: 0.8444 (mtp) cc_final: 0.8200 (mtp)
REVERT: B  640 VAL cc_start: 0.8805 (t) cc_final: 0.8441 (m)
REVERT: B  692 MET cc_start: 0.8449 (mtp) cc_final: 0.8221 (mtt)
REVERT: B  693 ASP cc_start: 0.7776 (t0) cc_final: 0.7566 (t70)
REVERT: B  723 THR cc_start: 0.8068 (m) cc_final: 0.7866 (p)
REVERT: A   33 MET cc_start: 0.7626 (mmm) cc_final: 0.7398 (mmt)
REVERT: A   36 PHE cc_start: 0.7879 (m-10) cc_final: 0.7605 (m-10)
REVERT: A  133 LEU cc_start: 0.8408 (tp) cc_final: 0.8192 (tp)
REVERT: A  157 LEU cc_start: 0.8181 (tt) cc_final: 0.7703 (tp)
REVERT: A  198 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8092 (ttm-80)
REVERT: A  240 LEU cc_start: 0.8394 (tp) cc_final: 0.8039 (tp)
REVERT: A  355 LEU cc_start: 0.7789 (tp) cc_final: 0.7251 (tp)
REVERT: A  417 VAL cc_start: 0.7421 (t) cc_final: 0.7170 (p)
REVERT: A  565 LEU cc_start: 0.8285 (mt) cc_final: 0.7780 (mt)
REVERT: A  566 ASN cc_start: 0.8123 (t0) cc_final: 0.7462 (t0)
REVERT: A  590 GLN cc_start: 0.7848 (tp40) cc_final: 0.7638 (tp40)
REVERT: A  651 ASP cc_start: 0.8317 (t70) cc_final: 0.8116 (t0)
REVERT: A  692 MET cc_start: 0.8112 (mtm) cc_final: 0.7832 (mtp)
  outliers start: 26
  outliers final: 14
  residues processed: 306
  average time/residue: 0.3033
  time to fit residues: 121.5620
Evaluate side-chains
  278 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 264
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
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  557 ASN
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  419 VAL
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 88 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0010
   chunk 69 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    2.7792

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

Flipped N/Q/H residues before XYZ refinement:
B 602 ASN
B 734 GLN
A  74 HIS
A 254 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.117024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110674 restraints weight = 19632.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.29
r_work: 0.3272 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10499  Z= 0.264
  Angle     :  0.587   7.601  14227  Z= 0.306
  Chirality :  0.042   0.172   1630
  Planarity :  0.005   0.067   1852
  Dihedral  :  7.522 158.737   1511
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.61 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.22), residues: 1301
  helix:  2.64 (0.19), residues: 667
  sheet:  0.66 (0.39), residues: 174
  loop : -0.86 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 137 
 HIS   0.006   0.002   HIS A 370 
 PHE   0.015   0.002   PHE A 334 
 TYR   0.019   0.002   TYR A 635 
 ARG   0.006   0.001   ARG A 579 

*********************** 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
  300 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 270
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 ASP cc_start: 0.8014 (t0) cc_final: 0.7807 (t0)
REVERT: B  154 ARG cc_start: 0.7585 (ttm170) cc_final: 0.7348 (ttm170)
REVERT: B  180 TYR cc_start: 0.8076 (p90) cc_final: 0.7777 (p90)
REVERT: B  201 LEU cc_start: 0.8697 (tp) cc_final: 0.8470 (mm)
REVERT: B  229 ASN cc_start: 0.7297 (t0) cc_final: 0.6847 (p0)
REVERT: B  242 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7060 (tm-30)
REVERT: B  302 MET cc_start: 0.7666 (ptm) cc_final: 0.7391 (ptt)
REVERT: B  354 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7587 (mtt180)
REVERT: B  355 LEU cc_start: 0.8879 (tp) cc_final: 0.8603 (tp)
REVERT: B  386 ASP cc_start: 0.7226 (p0) cc_final: 0.6689 (p0)
REVERT: B  424 VAL cc_start: 0.8707 (t) cc_final: 0.8485 (p)
REVERT: B  624 MET cc_start: 0.8354 (mtp) cc_final: 0.8154 (mtp)
REVERT: B  640 VAL cc_start: 0.8796 (t) cc_final: 0.8460 (m)
REVERT: B  693 ASP cc_start: 0.7841 (t0) cc_final: 0.7562 (t70)
REVERT: B  723 THR cc_start: 0.8020 (m) cc_final: 0.7757 (p)
REVERT: B  734 GLN cc_start: 0.8145 (mt0) cc_final: 0.7808 (mt0)
REVERT: B  784 GLU cc_start: 0.7120 (tp30) cc_final: 0.6883 (tp30)
REVERT: A   33 MET cc_start: 0.7675 (mmm) cc_final: 0.7425 (mmt)
REVERT: A   36 PHE cc_start: 0.7945 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  182 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7000 (pt0)
REVERT: A  198 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7860 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7767 (tp) cc_final: 0.7321 (tp)
REVERT: A  417 VAL cc_start: 0.7500 (t) cc_final: 0.7244 (p)
REVERT: A  566 ASN cc_start: 0.8114 (t0) cc_final: 0.7442 (t0)
REVERT: A  589 GLU cc_start: 0.7830 (tt0) cc_final: 0.7529 (pt0)
REVERT: A  692 MET cc_start: 0.8089 (mtm) cc_final: 0.7830 (mtp)
REVERT: A  788 ARG cc_start: 0.7789 (tpt90) cc_final: 0.7575 (tpt90)
  outliers start: 30
  outliers final: 21
  residues processed: 285
  average time/residue: 0.3021
  time to fit residues: 112.5911
Evaluate side-chains
  277 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 255
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
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  304 SER
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  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  568 THR
Chi-restraints excluded: chain A residue  695 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 127 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    3.5988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.115156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.108683 restraints weight = 19457.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.31
r_work: 0.3233 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10499  Z= 0.321
  Angle     :  0.609   9.517  14227  Z= 0.312
  Chirality :  0.042   0.167   1630
  Planarity :  0.005   0.072   1852
  Dihedral  :  7.433 159.683   1511
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.53 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.22), residues: 1301
  helix:  2.39 (0.19), residues: 667
  sheet:  0.50 (0.39), residues: 174
  loop : -0.96 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 137 
 HIS   0.006   0.002   HIS A 585 
 PHE   0.014   0.002   PHE A 725 
 TYR   0.018   0.002   TYR A  31 
 ARG   0.006   0.001   ARG B 667 

*********************** 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
  297 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 258
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7399 (ttm170)
REVERT: B  201 LEU cc_start: 0.8767 (tp) cc_final: 0.8369 (mm)
REVERT: B  229 ASN cc_start: 0.7318 (t0) cc_final: 0.6886 (p0)
REVERT: B  242 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7024 (tm-30)
REVERT: B  302 MET cc_start: 0.7699 (ptm) cc_final: 0.7436 (ptt)
REVERT: B  350 ARG cc_start: 0.6793 (ttp-110) cc_final: 0.6110 (ttp80)
REVERT: B  386 ASP cc_start: 0.7239 (p0) cc_final: 0.6734 (p0)
REVERT: B  579 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7526 (mtm180)
REVERT: B  640 VAL cc_start: 0.8843 (t) cc_final: 0.8548 (m)
REVERT: B  662 ASP cc_start: 0.7951 (p0) cc_final: 0.7621 (p0)
REVERT: B  693 ASP cc_start: 0.7852 (t0) cc_final: 0.7549 (t0)
REVERT: B  738 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8157 (mtmm)
REVERT: B  750 LEU cc_start: 0.8345 (tp) cc_final: 0.8129 (pp)
REVERT: B  784 GLU cc_start: 0.7158 (tp30) cc_final: 0.6908 (tp30)
REVERT: A  198 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7918 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7758 (tp) cc_final: 0.7338 (tp)
REVERT: A  417 VAL cc_start: 0.7592 (t) cc_final: 0.7348 (p)
REVERT: A  566 ASN cc_start: 0.8142 (t0) cc_final: 0.7476 (t0)
REVERT: A  575 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7447 (ttmm)
REVERT: A  589 GLU cc_start: 0.7867 (tt0) cc_final: 0.7601 (pt0)
REVERT: A  692 MET cc_start: 0.8105 (mtm) cc_final: 0.7841 (mtp)
REVERT: A  795 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7795 (tm-30)
  outliers start: 39
  outliers final: 27
  residues processed: 279
  average time/residue: 0.2999
  time to fit residues: 109.5903
Evaluate side-chains
  274 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 246
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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  270 ASP
Chi-restraints excluded: chain B residue  304 SER
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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  748 ASP
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  260 MET
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  617 MET
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  723 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.114676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108243 restraints weight = 19515.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.31
r_work: 0.3230 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10499  Z= 0.317
  Angle     :  0.598   9.688  14227  Z= 0.307
  Chirality :  0.042   0.160   1630
  Planarity :  0.005   0.069   1852
  Dihedral  :  7.366 159.280   1511
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.00 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.80 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.22), residues: 1301
  helix:  2.27 (0.19), residues: 666
  sheet:  0.41 (0.40), residues: 170
  loop : -1.04 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 137 
 HIS   0.006   0.002   HIS A 585 
 PHE   0.028   0.002   PHE A  36 
 TYR   0.019   0.002   TYR A  31 
 ARG   0.010   0.001   ARG B 667 

*********************** 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
  302 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 260
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7438 (ttm170)
REVERT: B  201 LEU cc_start: 0.8829 (tp) cc_final: 0.8551 (mm)
REVERT: B  229 ASN cc_start: 0.7401 (t0) cc_final: 0.6888 (p0)
REVERT: B  302 MET cc_start: 0.7715 (ptm) cc_final: 0.7441 (ptt)
REVERT: B  334 PHE cc_start: 0.8049 (m-10) cc_final: 0.7517 (m-80)
REVERT: B  350 ARG cc_start: 0.6902 (ttp-110) cc_final: 0.6513 (ttp80)
REVERT: B  373 GLN cc_start: 0.7885 (mm110) cc_final: 0.7536 (mm-40)
REVERT: B  565 LEU cc_start: 0.8265 (mt) cc_final: 0.8040 (mt)
REVERT: B  579 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7479 (mtm180)
REVERT: B  640 VAL cc_start: 0.8852 (t) cc_final: 0.8544 (m)
REVERT: B  693 ASP cc_start: 0.7862 (t0) cc_final: 0.7632 (t0)
REVERT: B  723 THR cc_start: 0.7977 (m) cc_final: 0.7691 (p)
REVERT: B  738 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8127 (mtmm)
REVERT: B  750 LEU cc_start: 0.8376 (tp) cc_final: 0.8173 (pp)
REVERT: B  784 GLU cc_start: 0.7200 (tp30) cc_final: 0.6946 (tp30)
REVERT: A   82 LYS cc_start: 0.8474 (mttm) cc_final: 0.8174 (mttt)
REVERT: A  166 MET cc_start: 0.7986 (tpp) cc_final: 0.7573 (tpp)
REVERT: A  198 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7853 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7730 (tp) cc_final: 0.7337 (tp)
REVERT: A  412 ILE cc_start: 0.8193 (pt) cc_final: 0.7968 (pt)
REVERT: A  417 VAL cc_start: 0.7591 (t) cc_final: 0.7344 (p)
REVERT: A  566 ASN cc_start: 0.8162 (t0) cc_final: 0.7492 (t0)
REVERT: A  575 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7459 (ttmm)
REVERT: A  589 GLU cc_start: 0.7868 (tt0) cc_final: 0.7637 (pt0)
REVERT: A  692 MET cc_start: 0.8119 (mtm) cc_final: 0.7846 (mtp)
  outliers start: 42
  outliers final: 31
  residues processed: 282
  average time/residue: 0.3141
  time to fit residues: 115.9645
Evaluate side-chains
  281 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 249
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
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  196 LEU
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  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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
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 B residue  778 LEU
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  170 LEU
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  419 VAL
Chi-restraints excluded: chain A residue  513 VAL
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  796 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 120 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0370
   chunk 44 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    4.6066

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.116000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109616 restraints weight = 19624.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.33
r_work: 0.3216 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.4062

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= 0.394
  Angle     :  0.649  10.598  14227  Z= 0.331
  Chirality :  0.043   0.164   1630
  Planarity :  0.005   0.066   1852
  Dihedral  :  7.475 157.959   1511
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.15 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.27 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1301
  helix:  2.06 (0.19), residues: 661
  sheet:  0.22 (0.40), residues: 170
  loop : -1.12 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 137 
 HIS   0.008   0.002   HIS A 585 
 PHE   0.033   0.002   PHE A  36 
 TYR   0.019   0.002   TYR A 635 
 ARG   0.012   0.001   ARG B 667 

*********************** 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
  306 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 267
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8900 (tp) cc_final: 0.8605 (tp)
REVERT: B  205 GLU cc_start: 0.7039 (mp0) cc_final: 0.6660 (mp0)
REVERT: B  229 ASN cc_start: 0.7392 (t0) cc_final: 0.6866 (p0)
REVERT: B  302 MET cc_start: 0.7670 (ptm) cc_final: 0.7397 (ptt)
REVERT: B  334 PHE cc_start: 0.7994 (m-10) cc_final: 0.7545 (m-80)
REVERT: B  393 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7707 (mp)
REVERT: B  579 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7354 (mtm180)
REVERT: B  640 VAL cc_start: 0.8865 (t) cc_final: 0.8537 (m)
REVERT: B  693 ASP cc_start: 0.7882 (t0) cc_final: 0.7631 (t0)
REVERT: B  738 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8155 (mtmm)
REVERT: B  784 GLU cc_start: 0.7296 (tp30) cc_final: 0.7039 (tp30)
REVERT: A   57 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7868 (mttm)
REVERT: A   82 LYS cc_start: 0.8493 (mttm) cc_final: 0.8190 (mttt)
REVERT: A  166 MET cc_start: 0.7956 (tpp) cc_final: 0.7644 (tpp)
REVERT: A  198 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8084 (ttm-80)
REVERT: A  355 LEU cc_start: 0.7804 (tp) cc_final: 0.7447 (tp)
REVERT: A  368 MET cc_start: 0.8053 (ttm) cc_final: 0.7832 (mtp)
REVERT: A  412 ILE cc_start: 0.8269 (pt) cc_final: 0.8034 (pt)
REVERT: A  417 VAL cc_start: 0.7641 (t) cc_final: 0.7412 (p)
REVERT: A  566 ASN cc_start: 0.8145 (t0) cc_final: 0.7469 (t0)
REVERT: A  575 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7484 (ttmm)
REVERT: A  589 GLU cc_start: 0.7876 (tt0) cc_final: 0.7662 (pt0)
REVERT: A  692 MET cc_start: 0.8192 (mtm) cc_final: 0.7930 (mtp)
  outliers start: 39
  outliers final: 31
  residues processed: 291
  average time/residue: 0.3180
  time to fit residues: 121.3578
Evaluate side-chains
  292 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 258
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
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  270 ASP
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  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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  663 LEU
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 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   57 LYS
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  315 VAL
Chi-restraints excluded: chain A residue  395 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 101 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    2.9988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.114897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108329 restraints weight = 19842.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.39
r_work: 0.3222 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10499  Z= 0.286
  Angle     :  0.607  10.171  14227  Z= 0.309
  Chirality :  0.041   0.144   1630
  Planarity :  0.005   0.069   1852
  Dihedral  :  7.363 158.703   1511
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.23 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.00 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.23), residues: 1301
  helix:  2.20 (0.19), residues: 661
  sheet:  0.04 (0.38), residues: 184
  loop : -1.03 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 137 
 HIS   0.008   0.001   HIS B 752 
 PHE   0.014   0.002   PHE A 334 
 TYR   0.018   0.001   TYR A  31 
 ARG   0.008   0.001   ARG B 667 

*********************** 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
  301 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 265
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 ARG cc_start: 0.8294 (mtp180) cc_final: 0.8079 (mtp180)
REVERT: B  201 LEU cc_start: 0.8895 (tp) cc_final: 0.8625 (tp)
REVERT: B  205 GLU cc_start: 0.7086 (mp0) cc_final: 0.6695 (mp0)
REVERT: B  229 ASN cc_start: 0.7473 (t0) cc_final: 0.7104 (p0)
REVERT: B  302 MET cc_start: 0.7616 (ptm) cc_final: 0.7318 (ptt)
REVERT: B  334 PHE cc_start: 0.7990 (m-10) cc_final: 0.7559 (m-80)
REVERT: B  350 ARG cc_start: 0.6704 (ttp80) cc_final: 0.6464 (ttp80)
REVERT: B  373 GLN cc_start: 0.7933 (mm110) cc_final: 0.7579 (mm-40)
REVERT: B  393 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: B  640 VAL cc_start: 0.8856 (t) cc_final: 0.8520 (m)
REVERT: B  661 ASP cc_start: 0.7802 (p0) cc_final: 0.7564 (p0)
REVERT: B  667 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7614 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7870 (t0) cc_final: 0.7623 (t0)
REVERT: B  723 THR cc_start: 0.7972 (m) cc_final: 0.7709 (p)
REVERT: B  784 GLU cc_start: 0.7255 (tp30) cc_final: 0.7003 (tp30)
REVERT: A   82 LYS cc_start: 0.8471 (mttm) cc_final: 0.8190 (mttt)
REVERT: A  166 MET cc_start: 0.8055 (tpp) cc_final: 0.7623 (tpp)
REVERT: A  198 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8082 (ttm-80)
REVERT: A  261 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7258 (mm-30)
REVERT: A  355 LEU cc_start: 0.7729 (tp) cc_final: 0.7375 (tp)
REVERT: A  412 ILE cc_start: 0.8210 (pt) cc_final: 0.8001 (pt)
REVERT: A  417 VAL cc_start: 0.7701 (t) cc_final: 0.7479 (p)
REVERT: A  566 ASN cc_start: 0.8129 (t0) cc_final: 0.7493 (t0)
REVERT: A  589 GLU cc_start: 0.7874 (tt0) cc_final: 0.7673 (pt0)
REVERT: A  692 MET cc_start: 0.8194 (mtm) cc_final: 0.7914 (mtp)
  outliers start: 36
  outliers final: 29
  residues processed: 284
  average time/residue: 0.3285
  time to fit residues: 122.4872
Evaluate side-chains
  289 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 259
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
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  322 LEU
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  393 LEU
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  691 LEU
Chi-restraints excluded: chain B residue  739 MET
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   57 LYS
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  513 VAL
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  768 SER
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 108 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0670
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 121 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.0126

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.122274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.115231 restraints weight = 19516.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.49
r_work: 0.3252 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10499  Z= 0.171
  Angle     :  0.562  10.596  14227  Z= 0.287
  Chirality :  0.038   0.133   1630
  Planarity :  0.005   0.057   1852
  Dihedral  :  7.143 159.318   1511
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.92 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.23), residues: 1301
  helix:  2.58 (0.20), residues: 659
  sheet:  0.10 (0.39), residues: 181
  loop : -0.91 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 137 
 HIS   0.005   0.001   HIS A 254 
 PHE   0.022   0.001   PHE A  36 
 TYR   0.017   0.001   TYR A  31 
 ARG   0.014   0.001   ARG A 163 

*********************** 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
  285 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 257
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7517 (ttm-80)
REVERT: B  201 LEU cc_start: 0.8901 (tp) cc_final: 0.8659 (tp)
REVERT: B  205 GLU cc_start: 0.7024 (mp0) cc_final: 0.6671 (mp0)
REVERT: B  229 ASN cc_start: 0.7444 (t0) cc_final: 0.6875 (p0)
REVERT: B  302 MET cc_start: 0.7450 (ptm) cc_final: 0.7144 (ptt)
REVERT: B  350 ARG cc_start: 0.6654 (ttp80) cc_final: 0.6297 (ttp80)
REVERT: B  354 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7530 (mtt180)
REVERT: B  373 GLN cc_start: 0.7932 (mm110) cc_final: 0.7571 (mm-40)
REVERT: B  579 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7328 (mtm180)
REVERT: B  635 TYR cc_start: 0.8204 (m-80) cc_final: 0.7957 (m-80)
REVERT: B  640 VAL cc_start: 0.8746 (t) cc_final: 0.8424 (m)
REVERT: B  661 ASP cc_start: 0.7855 (p0) cc_final: 0.7596 (p0)
REVERT: B  667 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7571 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7866 (t0) cc_final: 0.7626 (t0)
REVERT: B  723 THR cc_start: 0.7938 (m) cc_final: 0.7727 (p)
REVERT: B  738 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8134 (mtmm)
REVERT: B  784 GLU cc_start: 0.7186 (tp30) cc_final: 0.6896 (tp30)
REVERT: A   82 LYS cc_start: 0.8383 (mttm) cc_final: 0.8158 (mtmt)
REVERT: A  166 MET cc_start: 0.8101 (tpp) cc_final: 0.7887 (tpp)
REVERT: A  190 ILE cc_start: 0.8498 (mm) cc_final: 0.8275 (tt)
REVERT: A  198 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8052 (ttm-80)
REVERT: A  219 THR cc_start: 0.8707 (m) cc_final: 0.8384 (p)
REVERT: A  417 VAL cc_start: 0.7777 (t) cc_final: 0.7557 (p)
REVERT: A  566 ASN cc_start: 0.8129 (t0) cc_final: 0.7537 (t0)
REVERT: A  692 MET cc_start: 0.8193 (mtm) cc_final: 0.7922 (mtp)
  outliers start: 28
  outliers final: 23
  residues processed: 270
  average time/residue: 0.3106
  time to fit residues: 109.1425
Evaluate side-chains
  275 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 251
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  748 ASP
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   57 LYS
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  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  796 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0570
   chunk 90 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0170
   overall best weight:    1.3940

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.118873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112445 restraints weight = 19721.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.33
r_work: 0.3275 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10499  Z= 0.198
  Angle     :  0.585  10.979  14227  Z= 0.297
  Chirality :  0.039   0.130   1630
  Planarity :  0.005   0.053   1852
  Dihedral  :  7.067 157.884   1511
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.92 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.48 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.23), residues: 1301
  helix:  2.58 (0.20), residues: 664
  sheet:  0.23 (0.39), residues: 181
  loop : -0.93 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 137 
 HIS   0.006   0.001   HIS A 254 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.017   0.001   TYR A  31 
 ARG   0.008   0.001   ARG B 220 

*********************** 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
  283 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 255
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7477 (ttm-80)
REVERT: B  201 LEU cc_start: 0.8883 (tp) cc_final: 0.8653 (tp)
REVERT: B  205 GLU cc_start: 0.6968 (mp0) cc_final: 0.6628 (mp0)
REVERT: B  229 ASN cc_start: 0.7298 (t0) cc_final: 0.6749 (p0)
REVERT: B  302 MET cc_start: 0.7453 (ptm) cc_final: 0.7168 (ptt)
REVERT: B  350 ARG cc_start: 0.6575 (ttp80) cc_final: 0.6187 (ttp80)
REVERT: B  354 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7461 (mtt180)
REVERT: B  373 GLN cc_start: 0.7876 (mm110) cc_final: 0.7543 (mm-40)
REVERT: B  579 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7241 (mtm180)
REVERT: B  640 VAL cc_start: 0.8821 (t) cc_final: 0.8460 (m)
REVERT: B  661 ASP cc_start: 0.7821 (p0) cc_final: 0.7581 (p0)
REVERT: B  667 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7549 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7868 (t0) cc_final: 0.7492 (t0)
REVERT: B  738 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8167 (mtmm)
REVERT: B  784 GLU cc_start: 0.7132 (tp30) cc_final: 0.6844 (tp30)
REVERT: A   33 MET cc_start: 0.7610 (mmm) cc_final: 0.7276 (mmm)
REVERT: A  166 MET cc_start: 0.8026 (tpp) cc_final: 0.7690 (tpp)
REVERT: A  198 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8023 (ttm-80)
REVERT: A  219 THR cc_start: 0.8698 (m) cc_final: 0.8380 (p)
REVERT: A  566 ASN cc_start: 0.8066 (t0) cc_final: 0.7482 (t0)
REVERT: A  692 MET cc_start: 0.8178 (mtm) cc_final: 0.7904 (mtp)
  outliers start: 28
  outliers final: 26
  residues processed: 270
  average time/residue: 0.2868
  time to fit residues: 102.1139
Evaluate side-chains
  275 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 248
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
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  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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
Chi-restraints excluded: chain B residue  739 MET
Chi-restraints excluded: chain B residue  748 ASP
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   57 LYS
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  513 VAL
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  768 SER
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 105 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0070
   overall best weight:    1.0800

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.121442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114938 restraints weight = 19381.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.30
r_work: 0.3284 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10499  Z= 0.181
  Angle     :  0.580  11.656  14227  Z= 0.292
  Chirality :  0.038   0.189   1630
  Planarity :  0.004   0.051   1852
  Dihedral  :  7.018 157.769   1511
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.84 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.23), residues: 1301
  helix:  2.69 (0.20), residues: 660
  sheet:  0.09 (0.37), residues: 204
  loop : -0.89 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 137 
 HIS   0.005   0.001   HIS A 254 
 PHE   0.009   0.001   PHE A 725 
 TYR   0.017   0.001   TYR A  31 
 ARG   0.008   0.001   ARG B 220 

********************** 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
  283 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 255
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7480 (ttm-80)
REVERT: B  201 LEU cc_start: 0.8860 (tp) cc_final: 0.8644 (tp)
REVERT: B  205 GLU cc_start: 0.6941 (mp0) cc_final: 0.6612 (mp0)
REVERT: B  229 ASN cc_start: 0.7212 (t0) cc_final: 0.6681 (p0)
REVERT: B  302 MET cc_start: 0.7390 (ptm) cc_final: 0.7119 (ptt)
REVERT: B  350 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6356 (ttp80)
REVERT: B  579 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7249 (mtm180)
REVERT: B  640 VAL cc_start: 0.8784 (t) cc_final: 0.8446 (m)
REVERT: B  656 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6824 (tpt90)
REVERT: B  667 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7551 (mtm-85)
REVERT: B  693 ASP cc_start: 0.7830 (t0) cc_final: 0.7470 (t0)
REVERT: B  734 GLN cc_start: 0.8032 (mt0) cc_final: 0.7652 (mt0)
REVERT: B  738 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8104 (mtmm)
REVERT: B  784 GLU cc_start: 0.7103 (tp30) cc_final: 0.6859 (tp30)
REVERT: A  166 MET cc_start: 0.8043 (tpp) cc_final: 0.7709 (tpp)
REVERT: A  198 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8013 (ttm-80)
REVERT: A  219 THR cc_start: 0.8680 (m) cc_final: 0.8368 (p)
REVERT: A  566 ASN cc_start: 0.7996 (t0) cc_final: 0.7513 (t0)
REVERT: A  692 MET cc_start: 0.8169 (mtm) cc_final: 0.7887 (mtp)
REVERT: A  695 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7950 (pt)
  outliers start: 28
  outliers final: 26
  residues processed: 269
  average time/residue: 0.2974
  time to fit residues: 104.7525
Evaluate side-chains
  281 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 253
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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  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  579 ARG
Chi-restraints excluded: chain B residue  645 VAL
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   57 LYS
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  355 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  609 MET
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  768 SER
Chi-restraints excluded: chain A residue  796 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 102 optimal weight:    0.0770
   chunk 27 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 22 optimal weight:    0.4980
   chunk 90 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 118 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.7298

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.120989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114471 restraints weight = 19419.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.35
r_work: 0.3297 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.4604

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= 0.169
  Angle     :  0.570  11.579  14227  Z= 0.287
  Chirality :  0.038   0.131   1630
  Planarity :  0.004   0.043   1852
  Dihedral  :  6.920 157.328   1511
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.00 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.40 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.23), residues: 1301
  helix:  2.80 (0.20), residues: 660
  sheet:  0.12 (0.37), residues: 204
  loop : -0.86 (0.27), residues: 437

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

===============================================================================
Job complete
usr+sys time: 4765.25 seconds
wall clock time: 85 minutes 13.36 seconds (5113.36 seconds total)