Starting phenix.real_space_refine
on Wed Mar  4 03:27:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ou0_13071/03_2026/7ou0_13071.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.009
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: 7
    Type Number    sf(0)   Gaussians
     V       2      8.30       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      51      5.16       5
     C    6472      2.51       5
     N    1839      2.21       5
     O    1965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10335
  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: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 38
          Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.63, per 1000 atoms: 0.25
  Number of scatterers: 10335
  At special positions: 0
  Unit cell: (113.52, 121.44, 97.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     V       2     22.97
     S      51     16.00
     P       4     15.00
     Mg      2     11.99
     O    1965      8.00
     N    1839      7.00
     C    6472      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 543.1 milliseconds
  

  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
      55.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.728A  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: 3.696A  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: 3.639A  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: 3.777A  pdb=" N   THR B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
      removed outlier: 3.543A  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: 4.056A  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: 4.019A  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: 3.610A  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: 3.518A  pdb=" N   GLN A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.637A  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: 3.509A  pdb=" N   THR A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.586A  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: 3.788A  pdb=" N   GLN A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 635
      removed outlier: 3.568A  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: 3.621A  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: 3.508A  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: 5.900A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 5.827A  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: 3.639A  pdb=" N   LYS B 644 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 4.545A  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: 6.223A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ASP B 693 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ARG B 656 " --> pdb=" O   ASP B 693 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU B 610 " --> pdb=" O   PHE B 725 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ALA B 749 " --> pdb=" O   THR B 613 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   SER B 761 " --> pdb=" O   ASP B 748 " (cutoff:3.500A)
      removed outlier: 8.766A  pdb=" N   LEU B 750 " --> pdb=" O   MET B 759 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   MET B 759 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 58
      removed outlier: 5.207A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG A 112 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.632A  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: 6.333A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A 181 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 7.291A  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: 6.313A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 644 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU A 582 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 5.262A  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: 6.132A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ASP A 693 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ARG A 656 " --> pdb=" O   ASP A 693 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   ASN A 744 " --> pdb=" O   GLN A 763 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   GLN A 763 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   HIS A 746 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   SER A 761 " --> pdb=" O   HIS A 746 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASP A 748 " --> pdb=" O   MET A 759 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1641 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 3181
        1.34 -     1.48: 1487
        1.48 -     1.62: 5732
        1.62 -     1.76: 0
        1.76 -     1.90: 99
  Bond restraints: 10499
  Sorted by residual:
  bond pdb=" C4  ADP A 903 "
       pdb=" C5  ADP A 903 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C4  ADP B1002 "
       pdb=" C5  ADP B1002 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" N   ILE A  66 "
       pdb=" CA  ILE A  66 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.033 7.60e-03 1.73e+04 1.94e+01
  bond pdb=" N   ASN A 174 "
       pdb=" CA  ASN A 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 7.40e-03 1.83e+04 1.88e+01
  bond pdb=" N   ARG B 199 "
       pdb=" CA  ARG B 199 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 8.30e-03 1.45e+04 1.82e+01
  ... (remaining 10494 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 12504
        2.73 -     5.46: 1658
        5.46 -     8.20: 46
        8.20 -    10.93: 15
       10.93 -    13.66: 2
  Bond angle restraints: 14225
  Sorted by residual:
  angle pdb=" CA  PHE A 725 "
        pdb=" CB  PHE A 725 "
        pdb=" CG  PHE A 725 "
      ideal   model   delta    sigma   weight residual
     113.80  120.22   -6.42 1.00e+00 1.00e+00 4.12e+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  121.56   -8.16 1.34e+00 5.57e-01 3.71e+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  103.64    9.42 1.59e+00 3.96e-01 3.51e+01
  angle pdb=" N   GLU B 263 "
        pdb=" CA  GLU B 263 "
        pdb=" C   GLU B 263 "
      ideal   model   delta    sigma   weight residual
     111.87  103.88    7.99 1.41e+00 5.03e-01 3.21e+01
  angle pdb=" N   PRO A 605 "
        pdb=" CA  PRO A 605 "
        pdb=" C   PRO A 605 "
      ideal   model   delta    sigma   weight residual
     113.65  106.31    7.34 1.35e+00 5.49e-01 2.96e+01
  ... (remaining 14220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 6287
       35.45 -    70.91: 128
       70.91 -   106.36: 15
      106.36 -   141.82: 1
      141.82 -   177.27: 2
  Dihedral angle restraints: 6433
    sinusoidal: 2634
      harmonic: 3799
  Sorted by residual:
  dihedral pdb=" O1B ADP B1002 "
           pdb=" O3A ADP B1002 "
           pdb=" PB  ADP B1002 "
           pdb=" PA  ADP B1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  117.27 -177.27     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" O2A ADP B1002 "
           pdb=" O3A ADP B1002 "
           pdb=" PA  ADP B1002 "
           pdb=" PB  ADP B1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   82.70 -142.70     1      2.00e+01 2.50e-03 4.31e+01
  dihedral pdb=" C5' ADP B1002 "
           pdb=" O5' ADP B1002 "
           pdb=" PA  ADP B1002 "
           pdb=" O2A ADP B1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  173.49  126.52     1      2.00e+01 2.50e-03 3.83e+01
  ... (remaining 6430 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 769
       0.075 -    0.150: 567
       0.150 -    0.226: 228
       0.226 -    0.301: 65
       0.301 -    0.376: 3
  Chirality restraints: 1632
  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    0.38 2.00e-01 2.50e+01 3.53e+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    2.76   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  LEU A 133 "
            pdb=" N   LEU A 133 "
            pdb=" C   LEU A 133 "
            pdb=" CB  LEU A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1629 not shown)

  Planarity restraints: 1852
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 336 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.85e+00
        pdb=" C   ALA B 336 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ALA B 336 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLY B 337 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 268 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.84e+00
        pdb=" C   ILE B 268 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ILE B 268 "    0.016 2.00e-02 2.50e+03
        pdb=" N   MET B 269 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 250 "    0.011 2.00e-02 2.50e+03   2.36e-02 5.55e+00
        pdb=" C   THR B 250 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR B 250 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR B 251 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1849 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 11
        2.42 -     3.04: 5662
        3.04 -     3.66: 15928
        3.66 -     4.28: 23103
        4.28 -     4.90: 39303
  Nonbonded interactions: 84007
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 621 "
            pdb="MG    MG A 902 "
     model   vdw
     1.798 2.170
  nonbonded pdb=" OG  SER B 621 "
            pdb="MG    MG B1001 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" O   ILE A 597 "
            pdb=" N6  ADP A 903 "
     model   vdw
     2.233 3.120
  nonbonded pdb="MG    MG A 902 "
            pdb=" O2  VO4 A 904 "
     model   vdw
     2.241 2.170
  nonbonded pdb="MG    MG B1001 "
            pdb=" O3  VO4 A 901 "
     model   vdw
     2.251 2.170
  ... (remaining 84002 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.020
  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:          0.170
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     11.410
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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   0.110  10499  Z= 0.974
  Angle     :  1.765  13.659  14225  Z= 1.349
  Chirality :  0.112   0.376   1632
  Planarity :  0.006   0.036   1852
  Dihedral  : 15.367 177.269   3975
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  7.93 %
    Favored  : 91.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.21), residues: 1301
  helix:  3.41 (0.17), residues: 661
  sheet:  0.89 (0.39), residues: 157
  loop : -0.28 (0.24), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 354 
 TYR   0.030   0.003   TYR A  31 
 PHE   0.030   0.004   PHE A 725 
 TRP   0.019   0.003   TRP B 202 
 HIS   0.008   0.002   HIS B 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.01288 (10499)
  covalent geometry    : angle       1.76548 (14225)
  hydrogen bonds       : bond        0.20127 (  567)
  hydrogen bonds       : angle       6.12952 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 431
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 THR cc_start: 0.8830 (t) cc_final: 0.8537 (m)
REVERT: B  180 TYR cc_start: 0.8306 (p90) cc_final: 0.7936 (p90)
REVERT: B  208 THR cc_start: 0.7703 (m) cc_final: 0.6696 (m)
REVERT: B  242 GLN cc_start: 0.8612 (tp40) cc_final: 0.8380 (tp-100)
REVERT: B  349 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7923 (mt-10)
REVERT: B  359 THR cc_start: 0.8523 (m) cc_final: 0.8259 (p)
REVERT: B  420 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7783 (ttp80)
REVERT: B  538 HIS cc_start: 0.8824 (m-70) cc_final: 0.8288 (m90)
REVERT: A   43 ASP cc_start: 0.8622 (m-30) cc_final: 0.8165 (m-30)
REVERT: A  115 THR cc_start: 0.9224 (p) cc_final: 0.8984 (t)
REVERT: A  125 LEU cc_start: 0.8096 (mt) cc_final: 0.7870 (mt)
REVERT: A  129 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8360 (mm-40)
REVERT: A  204 PHE cc_start: 0.8104 (m-80) cc_final: 0.7801 (m-10)
REVERT: A  275 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8476 (tpp-160)
REVERT: A  739 MET cc_start: 0.8586 (ttp) cc_final: 0.8200 (ttt)
REVERT: A  740 GLU cc_start: 0.8387 (tt0) cc_final: 0.8163 (mm-30)
REVERT: A  752 HIS cc_start: 0.7925 (t-90) cc_final: 0.7592 (t-90)
  outliers start: 1
  outliers final: 0
  residues processed: 432
  average time/residue: 0.1384
  time to fit residues: 77.1543
Evaluate side-chains
  206 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
B 538 HIS
B 590 GLN
B 643 GLN
B 791 GLN
A 430 ASN
A 543 GLN
A 683 ASN
A 714 ASN
A 734 GLN
A 744 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.102546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088779 restraints weight = 22072.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091685 restraints weight = 10788.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093595 restraints weight = 6378.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094818 restraints weight = 4288.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.095675 restraints weight = 3189.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10499  Z= 0.170
  Angle     :  0.683  10.597  14225  Z= 0.343
  Chirality :  0.043   0.191   1632
  Planarity :  0.005   0.045   1852
  Dihedral  :  8.283 171.784   1469
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.31 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.22), residues: 1301
  helix:  2.88 (0.19), residues: 680
  sheet:  0.95 (0.38), residues: 183
  loop : -0.62 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 194 
 TYR   0.020   0.002   TYR B 623 
 PHE   0.018   0.002   PHE A 725 
 TRP   0.016   0.002   TRP A 202 
 HIS   0.012   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10499)
  covalent geometry    : angle       0.68314 (14225)
  hydrogen bonds       : bond        0.05069 (  567)
  hydrogen bonds       : angle       4.73982 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 193
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  171 GLN cc_start: 0.8316 (tp40) cc_final: 0.8115 (mp10)
REVERT: B  180 TYR cc_start: 0.7848 (p90) cc_final: 0.7497 (p90)
REVERT: B  405 ASP cc_start: 0.7927 (t70) cc_final: 0.7630 (t70)
REVERT: B  434 ASP cc_start: 0.7337 (m-30) cc_final: 0.7092 (m-30)
REVERT: B  517 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8379 (pptt)
REVERT: B  519 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8429 (pttt)
REVERT: B  538 HIS cc_start: 0.8241 (m90) cc_final: 0.7602 (m170)
REVERT: B  557 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8475 (t0)
REVERT: A   43 ASP cc_start: 0.8025 (m-30) cc_final: 0.7764 (m-30)
REVERT: A  115 THR cc_start: 0.9166 (p) cc_final: 0.8882 (t)
REVERT: A  278 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7979 (pm20)
REVERT: A  313 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7719 (mmm)
REVERT: A  734 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7922 (mp10)
REVERT: A  739 MET cc_start: 0.7611 (ttp) cc_final: 0.7281 (ttm)
  outliers start: 40
  outliers final: 19
  residues processed: 215
  average time/residue: 0.1075
  time to fit residues: 32.3462
Evaluate side-chains
  174 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   33 MET
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  734 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 110 optimal weight:    8.9990
   chunk 59 optimal weight:   20.0000
   chunk 130 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 626 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.100672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.086705 restraints weight = 22288.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.089577 restraints weight = 11010.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.091453 restraints weight = 6570.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.092700 restraints weight = 4449.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093522 restraints weight = 3320.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10499  Z= 0.163
  Angle     :  0.637   8.618  14225  Z= 0.314
  Chirality :  0.043   0.353   1632
  Planarity :  0.004   0.042   1852
  Dihedral  :  7.962 165.976   1469
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.51 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.22), residues: 1301
  helix:  2.73 (0.19), residues: 672
  sheet:  0.63 (0.38), residues: 181
  loop : -0.75 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 194 
 TYR   0.020   0.002   TYR B 623 
 PHE   0.016   0.002   PHE B 184 
 TRP   0.028   0.002   TRP B 436 
 HIS   0.006   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10499)
  covalent geometry    : angle       0.63670 (14225)
  hydrogen bonds       : bond        0.04396 (  567)
  hydrogen bonds       : angle       4.51083 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 174
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 PHE cc_start: 0.6521 (m-10) cc_final: 0.6026 (m-10)
REVERT: B  171 GLN cc_start: 0.8214 (tp40) cc_final: 0.7934 (mp10)
REVERT: B  196 LEU cc_start: 0.7410 (tt) cc_final: 0.7022 (mp)
REVERT: B  434 ASP cc_start: 0.7304 (m-30) cc_final: 0.7023 (m-30)
REVERT: B  517 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8391 (pptt)
REVERT: B  538 HIS cc_start: 0.8287 (m90) cc_final: 0.7661 (m170)
REVERT: B  561 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8038 (mmm160)
REVERT: A   13 MET cc_start: 0.8156 (ppp) cc_final: 0.7744 (ppp)
REVERT: A   43 ASP cc_start: 0.8104 (m-30) cc_final: 0.7850 (m-30)
REVERT: A   86 GLN cc_start: 0.8141 (mt0) cc_final: 0.7885 (mp10)
REVERT: A  115 THR cc_start: 0.9130 (p) cc_final: 0.8846 (t)
REVERT: A  149 ASP cc_start: 0.7432 (t0) cc_final: 0.7153 (t0)
REVERT: A  152 SER cc_start: 0.8465 (p) cc_final: 0.8120 (t)
REVERT: A  313 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7690 (mmm)
REVERT: A  319 ARG cc_start: 0.6811 (tpm170) cc_final: 0.6558 (tpp-160)
REVERT: A  671 MET cc_start: 0.8304 (tpp) cc_final: 0.8030 (tpp)
REVERT: A  714 ASN cc_start: 0.8606 (t0) cc_final: 0.8267 (t0)
REVERT: A  739 MET cc_start: 0.7765 (ttp) cc_final: 0.7311 (ttm)
  outliers start: 45
  outliers final: 28
  residues processed: 201
  average time/residue: 0.1042
  time to fit residues: 29.6528
Evaluate side-chains
  181 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 127 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 31 optimal weight:   30.0000
   chunk 117 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 119 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 242 GLN
A 381 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.090777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.076689 restraints weight = 23581.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.079336 restraints weight = 12005.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.081069 restraints weight = 7332.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.082234 restraints weight = 5068.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.082964 restraints weight = 3846.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10499  Z= 0.240
  Angle     :  0.674   9.631  14225  Z= 0.332
  Chirality :  0.044   0.171   1632
  Planarity :  0.005   0.052   1852
  Dihedral  :  7.980 163.669   1469
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 17.16 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.22), residues: 1301
  helix:  2.41 (0.19), residues: 668
  sheet:  0.21 (0.37), residues: 181
  loop : -0.81 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 194 
 TYR   0.024   0.002   TYR B 623 
 PHE   0.019   0.002   PHE B 654 
 TRP   0.034   0.003   TRP B 436 
 HIS   0.005   0.001   HIS B 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (10499)
  covalent geometry    : angle       0.67380 (14225)
  hydrogen bonds       : bond        0.04412 (  567)
  hydrogen bonds       : angle       4.55928 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 159
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  171 GLN cc_start: 0.8270 (tp40) cc_final: 0.7929 (mp10)
REVERT: B  180 TYR cc_start: 0.7847 (p90) cc_final: 0.6709 (p90)
REVERT: B  196 LEU cc_start: 0.7744 (tt) cc_final: 0.6935 (mp)
REVERT: B  434 ASP cc_start: 0.7645 (m-30) cc_final: 0.7357 (m-30)
REVERT: B  517 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8339 (pptt)
REVERT: B  538 HIS cc_start: 0.8421 (m90) cc_final: 0.7899 (m90)
REVERT: A   13 MET cc_start: 0.8353 (ppp) cc_final: 0.7835 (ppp)
REVERT: A   41 TYR cc_start: 0.8785 (m-80) cc_final: 0.8404 (m-80)
REVERT: A   43 ASP cc_start: 0.8221 (m-30) cc_final: 0.8005 (m-30)
REVERT: A  149 ASP cc_start: 0.7763 (t0) cc_final: 0.7495 (t0)
REVERT: A  152 SER cc_start: 0.8387 (p) cc_final: 0.8129 (t)
REVERT: A  281 GLN cc_start: 0.8998 (tt0) cc_final: 0.8668 (tt0)
REVERT: A  313 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7928 (tpp)
REVERT: A  714 ASN cc_start: 0.8651 (t0) cc_final: 0.8296 (t0)
REVERT: A  739 MET cc_start: 0.7865 (ttp) cc_final: 0.7500 (ttm)
  outliers start: 48
  outliers final: 35
  residues processed: 186
  average time/residue: 0.1011
  time to fit residues: 27.0179
Evaluate side-chains
  178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  711 CYS
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 119 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9990
   chunk 126 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 101 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 276 ASN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.075633 restraints weight = 23786.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.078279 restraints weight = 11981.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.080032 restraints weight = 7309.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.081216 restraints weight = 5043.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.082042 restraints weight = 3816.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10499  Z= 0.231
  Angle     :  0.672   8.801  14225  Z= 0.327
  Chirality :  0.043   0.170   1632
  Planarity :  0.005   0.043   1852
  Dihedral  :  7.984 165.404   1469
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.08 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.17 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.23), residues: 1301
  helix:  2.30 (0.19), residues: 667
  sheet:  0.07 (0.39), residues: 180
  loop : -0.85 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 409 
 TYR   0.024   0.002   TYR B 623 
 PHE   0.019   0.002   PHE B 725 
 TRP   0.026   0.002   TRP A 202 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 (10499)
  covalent geometry    : angle       0.67187 (14225)
  hydrogen bonds       : bond        0.04272 (  567)
  hydrogen bonds       : angle       4.51894 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 154
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.8052 (p90) cc_final: 0.6902 (p90)
REVERT: B  196 LEU cc_start: 0.7783 (tt) cc_final: 0.6952 (mp)
REVERT: B  221 ASP cc_start: 0.8010 (p0) cc_final: 0.7528 (p0)
REVERT: B  434 ASP cc_start: 0.7919 (m-30) cc_final: 0.7646 (m-30)
REVERT: B  517 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8276 (pptt)
REVERT: B  538 HIS cc_start: 0.8383 (m90) cc_final: 0.7937 (m90)
REVERT: B  622 THR cc_start: 0.8946 (m) cc_final: 0.8646 (p)
REVERT: A   13 MET cc_start: 0.8419 (ppp) cc_final: 0.8064 (ppp)
REVERT: A   41 TYR cc_start: 0.8902 (m-80) cc_final: 0.8076 (m-80)
REVERT: A   43 ASP cc_start: 0.8274 (m-30) cc_final: 0.8032 (m-30)
REVERT: A  109 LYS cc_start: 0.8692 (pttt) cc_final: 0.8481 (pttp)
REVERT: A  149 ASP cc_start: 0.7579 (t0) cc_final: 0.7359 (t0)
REVERT: A  281 GLN cc_start: 0.9046 (tt0) cc_final: 0.8697 (tt0)
REVERT: A  313 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7816 (tpp)
REVERT: A  404 ARG cc_start: 0.7726 (ptm160) cc_final: 0.7467 (ptm160)
REVERT: A  609 MET cc_start: 0.8813 (ttt) cc_final: 0.8553 (ttt)
REVERT: A  656 ARG cc_start: 0.7266 (tpm170) cc_final: 0.6832 (tpm170)
REVERT: A  714 ASN cc_start: 0.8673 (t0) cc_final: 0.8290 (t0)
  outliers start: 48
  outliers final: 35
  residues processed: 183
  average time/residue: 0.0981
  time to fit residues: 25.8742
Evaluate side-chains
  181 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   chunk 64 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 120 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 124 optimal weight:    0.3980
   overall best weight:    3.0788

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 GLN
B 276 ASN
A  24 HIS
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.091654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.077546 restraints weight = 23858.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.080199 restraints weight = 12074.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.081938 restraints weight = 7370.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.083126 restraints weight = 5098.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.083923 restraints weight = 3848.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.5446

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= 0.139
  Angle     :  0.611  13.093  14225  Z= 0.295
  Chirality :  0.040   0.155   1632
  Planarity :  0.004   0.043   1852
  Dihedral  :  7.825 168.586   1469
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.23 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.11 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.23), residues: 1301
  helix:  2.46 (0.20), residues: 679
  sheet:  0.02 (0.38), residues: 180
  loop : -0.76 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 409 
 TYR   0.019   0.001   TYR B 623 
 PHE   0.022   0.002   PHE B 184 
 TRP   0.022   0.002   TRP A 202 
 HIS   0.004   0.001   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10499)
  covalent geometry    : angle       0.61117 (14225)
  hydrogen bonds       : bond        0.03693 (  567)
  hydrogen bonds       : angle       4.34370 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 158
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.7893 (p90) cc_final: 0.6775 (p90)
REVERT: B  196 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6864 (mp)
REVERT: B  241 LEU cc_start: 0.9081 (tp) cc_final: 0.8829 (tp)
REVERT: B  434 ASP cc_start: 0.7908 (m-30) cc_final: 0.7607 (m-30)
REVERT: B  517 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (pptt)
REVERT: B  538 HIS cc_start: 0.8349 (m90) cc_final: 0.7984 (m90)
REVERT: B  622 THR cc_start: 0.8890 (m) cc_final: 0.8578 (p)
REVERT: A   13 MET cc_start: 0.8416 (ppp) cc_final: 0.8019 (ppp)
REVERT: A   41 TYR cc_start: 0.8844 (m-80) cc_final: 0.8381 (m-80)
REVERT: A   43 ASP cc_start: 0.8301 (m-30) cc_final: 0.8072 (m-30)
REVERT: A  281 GLN cc_start: 0.9033 (tt0) cc_final: 0.8559 (tt0)
REVERT: A  313 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7708 (tpp)
REVERT: A  531 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8405 (tp)
REVERT: A  656 ARG cc_start: 0.7195 (tpm170) cc_final: 0.6761 (tpm170)
REVERT: A  671 MET cc_start: 0.8210 (tpp) cc_final: 0.7800 (tpt)
REVERT: A  714 ASN cc_start: 0.8582 (t0) cc_final: 0.8138 (t0)
REVERT: A  794 ARG cc_start: 0.7674 (mtm180) cc_final: 0.6879 (mtm110)
  outliers start: 37
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1078
  time to fit residues: 27.5997
Evaluate side-chains
  173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  557 ASN
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  725 PHE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 70 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.089454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.075806 restraints weight = 23847.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.078268 restraints weight = 12435.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.079914 restraints weight = 7747.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.080973 restraints weight = 5420.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081752 restraints weight = 4162.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10499  Z= 0.236
  Angle     :  0.686  10.727  14225  Z= 0.330
  Chirality :  0.043   0.222   1632
  Planarity :  0.005   0.044   1852
  Dihedral  :  7.896 170.376   1469
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.46 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 20.11 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.23), residues: 1301
  helix:  2.27 (0.20), residues: 678
  sheet: -0.11 (0.38), residues: 180
  loop : -0.74 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 194 
 TYR   0.024   0.002   TYR B 623 
 PHE   0.016   0.002   PHE B 654 
 TRP   0.036   0.003   TRP A 202 
 HIS   0.004   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (10499)
  covalent geometry    : angle       0.68556 (14225)
  hydrogen bonds       : bond        0.04141 (  567)
  hydrogen bonds       : angle       4.48699 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 147
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.7942 (p90) cc_final: 0.6832 (p90)
REVERT: B  196 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6556 (mp)
REVERT: B  202 TRP cc_start: 0.8126 (p-90) cc_final: 0.7906 (p-90)
REVERT: B  221 ASP cc_start: 0.7984 (p0) cc_final: 0.7506 (p0)
REVERT: B  241 LEU cc_start: 0.9081 (tp) cc_final: 0.8836 (tp)
REVERT: B  434 ASP cc_start: 0.7908 (m-30) cc_final: 0.7601 (m-30)
REVERT: B  517 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8252 (pptt)
REVERT: B  538 HIS cc_start: 0.8420 (m90) cc_final: 0.8072 (m90)
REVERT: B  622 THR cc_start: 0.8975 (m) cc_final: 0.8667 (p)
REVERT: B  693 ASP cc_start: 0.7516 (t70) cc_final: 0.7266 (t0)
REVERT: A   13 MET cc_start: 0.8516 (ppp) cc_final: 0.8097 (ppp)
REVERT: A   41 TYR cc_start: 0.8918 (m-80) cc_final: 0.8333 (m-80)
REVERT: A   43 ASP cc_start: 0.8216 (m-30) cc_final: 0.7992 (m-30)
REVERT: A   86 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7731 (mp10)
REVERT: A  149 ASP cc_start: 0.7579 (t0) cc_final: 0.7267 (t0)
REVERT: A  281 GLN cc_start: 0.9040 (tt0) cc_final: 0.8814 (tt0)
REVERT: A  313 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7869 (tpp)
REVERT: A  404 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7720 (ptm160)
REVERT: A  656 ARG cc_start: 0.7286 (tpm170) cc_final: 0.6795 (tpm170)
REVERT: A  671 MET cc_start: 0.8334 (tpp) cc_final: 0.7883 (tpt)
REVERT: A  714 ASN cc_start: 0.8658 (t0) cc_final: 0.8245 (t0)
  outliers start: 46
  outliers final: 34
  residues processed: 174
  average time/residue: 0.0977
  time to fit residues: 24.9331
Evaluate side-chains
  178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain B residue  725 PHE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  755 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 125 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 115 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.091285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.077231 restraints weight = 23539.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.079868 restraints weight = 11940.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.081608 restraints weight = 7283.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.082776 restraints weight = 5023.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.083553 restraints weight = 3795.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10499  Z= 0.148
  Angle     :  0.628  10.442  14225  Z= 0.301
  Chirality :  0.041   0.176   1632
  Planarity :  0.004   0.042   1852
  Dihedral  :  7.811 174.581   1469
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.54 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.13 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.23), residues: 1301
  helix:  2.46 (0.20), residues: 673
  sheet: -0.19 (0.36), residues: 197
  loop : -0.69 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 194 
 TYR   0.019   0.001   TYR B 623 
 PHE   0.012   0.001   PHE B 725 
 TRP   0.026   0.002   TRP A 202 
 HIS   0.004   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10499)
  covalent geometry    : angle       0.62812 (14225)
  hydrogen bonds       : bond        0.03695 (  567)
  hydrogen bonds       : angle       4.37570 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.7871 (p90) cc_final: 0.6818 (p90)
REVERT: B  196 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6934 (mp)
REVERT: B  221 ASP cc_start: 0.7978 (p0) cc_final: 0.7492 (p0)
REVERT: B  241 LEU cc_start: 0.9059 (tp) cc_final: 0.8806 (tp)
REVERT: B  434 ASP cc_start: 0.7886 (m-30) cc_final: 0.7570 (m-30)
REVERT: B  517 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8155 (pptt)
REVERT: B  538 HIS cc_start: 0.8413 (m90) cc_final: 0.8081 (m90)
REVERT: B  622 THR cc_start: 0.8889 (m) cc_final: 0.8582 (p)
REVERT: B  693 ASP cc_start: 0.7506 (t70) cc_final: 0.7237 (t0)
REVERT: A   13 MET cc_start: 0.8466 (ppp) cc_final: 0.8012 (ppp)
REVERT: A   41 TYR cc_start: 0.8881 (m-80) cc_final: 0.8297 (m-80)
REVERT: A   43 ASP cc_start: 0.8190 (m-30) cc_final: 0.7930 (m-30)
REVERT: A  149 ASP cc_start: 0.7535 (t0) cc_final: 0.7171 (t0)
REVERT: A  281 GLN cc_start: 0.9039 (tt0) cc_final: 0.8598 (tt0)
REVERT: A  313 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7798 (tpp)
REVERT: A  404 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7642 (ptm160)
REVERT: A  531 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8409 (tp)
REVERT: A  539 LEU cc_start: 0.9037 (tp) cc_final: 0.8819 (tp)
REVERT: A  656 ARG cc_start: 0.7246 (tpm170) cc_final: 0.6765 (tpm170)
REVERT: A  671 MET cc_start: 0.8341 (tpp) cc_final: 0.7875 (tpt)
REVERT: A  714 ASN cc_start: 0.8601 (t0) cc_final: 0.8165 (t0)
REVERT: A  794 ARG cc_start: 0.7682 (mtm180) cc_final: 0.6984 (mtm180)
  outliers start: 38
  outliers final: 30
  residues processed: 182
  average time/residue: 0.1063
  time to fit residues: 27.5902
Evaluate side-chains
  179 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain B residue  725 PHE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  799 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 127 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   chunk 117 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 123 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.090613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.076608 restraints weight = 23793.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.079221 restraints weight = 12168.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.080934 restraints weight = 7447.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.082094 restraints weight = 5162.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.082888 restraints weight = 3911.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.5785

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= 0.186
  Angle     :  0.667  12.559  14225  Z= 0.317
  Chirality :  0.042   0.209   1632
  Planarity :  0.004   0.042   1852
  Dihedral  :  7.834 177.281   1469
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.07 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.68 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.23), residues: 1301
  helix:  2.37 (0.20), residues: 678
  sheet: -0.26 (0.36), residues: 197
  loop : -0.65 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 194 
 TYR   0.022   0.001   TYR B 623 
 PHE   0.012   0.002   PHE B 725 
 TRP   0.043   0.003   TRP A 202 
 HIS   0.003   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (10499)
  covalent geometry    : angle       0.66663 (14225)
  hydrogen bonds       : bond        0.03846 (  567)
  hydrogen bonds       : angle       4.41614 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.7864 (p90) cc_final: 0.6819 (p90)
REVERT: B  196 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6790 (mp)
REVERT: B  221 ASP cc_start: 0.7988 (p0) cc_final: 0.7522 (p0)
REVERT: B  241 LEU cc_start: 0.9074 (tp) cc_final: 0.8827 (tp)
REVERT: B  434 ASP cc_start: 0.7884 (m-30) cc_final: 0.7565 (m-30)
REVERT: B  517 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8153 (pptt)
REVERT: B  538 HIS cc_start: 0.8375 (m90) cc_final: 0.8032 (m90)
REVERT: B  609 MET cc_start: 0.8508 (tpp) cc_final: 0.8244 (tpp)
REVERT: B  622 THR cc_start: 0.8907 (m) cc_final: 0.8606 (p)
REVERT: B  693 ASP cc_start: 0.7507 (t70) cc_final: 0.7305 (t0)
REVERT: A   13 MET cc_start: 0.8433 (ppp) cc_final: 0.7982 (ppp)
REVERT: A   41 TYR cc_start: 0.8917 (m-80) cc_final: 0.8356 (m-80)
REVERT: A   43 ASP cc_start: 0.8203 (m-30) cc_final: 0.7966 (m-30)
REVERT: A   86 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7687 (mp10)
REVERT: A  149 ASP cc_start: 0.7597 (t0) cc_final: 0.7209 (t0)
REVERT: A  281 GLN cc_start: 0.9046 (tt0) cc_final: 0.8806 (tt0)
REVERT: A  313 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7881 (tpp)
REVERT: A  404 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7653 (ptm160)
REVERT: A  531 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8418 (tp)
REVERT: A  656 ARG cc_start: 0.7297 (tpm170) cc_final: 0.6795 (tpm170)
REVERT: A  671 MET cc_start: 0.8416 (tpp) cc_final: 0.7942 (tpt)
REVERT: A  714 ASN cc_start: 0.8565 (t0) cc_final: 0.8091 (t0)
  outliers start: 38
  outliers final: 30
  residues processed: 171
  average time/residue: 0.1034
  time to fit residues: 25.4348
Evaluate side-chains
  178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain B residue  725 PHE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  799 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 102 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 115 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 171 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.097847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.084210 restraints weight = 22482.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.086918 restraints weight = 11464.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.088717 restraints weight = 6991.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089877 restraints weight = 4802.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090698 restraints weight = 3628.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.5859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10499  Z= 0.172
  Angle     :  0.672  12.326  14225  Z= 0.321
  Chirality :  0.042   0.185   1632
  Planarity :  0.004   0.042   1852
  Dihedral  :  7.816 178.720   1469
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.69 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.49 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.23), residues: 1301
  helix:  2.39 (0.20), residues: 677
  sheet: -0.39 (0.36), residues: 203
  loop : -0.57 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 194 
 TYR   0.021   0.001   TYR B 623 
 PHE   0.010   0.001   PHE B 654 
 TRP   0.041   0.003   TRP A 202 
 HIS   0.004   0.001   HIS A 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10499)
  covalent geometry    : angle       0.67207 (14225)
  hydrogen bonds       : bond        0.03769 (  567)
  hydrogen bonds       : angle       4.40353 ( 1641)

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

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 TYR cc_start: 0.7898 (p90) cc_final: 0.6876 (p90)
REVERT: B  196 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6775 (mp)
REVERT: B  221 ASP cc_start: 0.7975 (p0) cc_final: 0.7514 (p0)
REVERT: B  241 LEU cc_start: 0.9094 (tp) cc_final: 0.8839 (tp)
REVERT: B  434 ASP cc_start: 0.7882 (m-30) cc_final: 0.7557 (m-30)
REVERT: B  517 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (pptt)
REVERT: B  538 HIS cc_start: 0.8311 (m90) cc_final: 0.7952 (m90)
REVERT: B  609 MET cc_start: 0.8512 (tpp) cc_final: 0.8220 (tpp)
REVERT: B  622 THR cc_start: 0.8905 (m) cc_final: 0.8618 (p)
REVERT: B  693 ASP cc_start: 0.7547 (t70) cc_final: 0.7296 (t0)
REVERT: A   13 MET cc_start: 0.8369 (ppp) cc_final: 0.7941 (ppp)
REVERT: A   41 TYR cc_start: 0.8949 (m-80) cc_final: 0.8384 (m-80)
REVERT: A   43 ASP cc_start: 0.8171 (m-30) cc_final: 0.7937 (m-30)
REVERT: A   86 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7756 (mp10)
REVERT: A  149 ASP cc_start: 0.7663 (t0) cc_final: 0.7260 (t0)
REVERT: A  281 GLN cc_start: 0.9003 (tt0) cc_final: 0.8585 (tt0)
REVERT: A  404 ARG cc_start: 0.7990 (ptm160) cc_final: 0.7689 (ptm160)
REVERT: A  531 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8389 (tp)
REVERT: A  539 LEU cc_start: 0.9061 (tp) cc_final: 0.8833 (tp)
REVERT: A  656 ARG cc_start: 0.7290 (tpm170) cc_final: 0.6807 (tpm170)
REVERT: A  671 MET cc_start: 0.8368 (tpp) cc_final: 0.7911 (tpt)
REVERT: A  714 ASN cc_start: 0.8467 (t0) cc_final: 0.8048 (t0)
  outliers start: 41
  outliers final: 30
  residues processed: 175
  average time/residue: 0.1026
  time to fit residues: 25.6882
Evaluate side-chains
  181 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  517 LYS
Chi-restraints excluded: chain B residue  535 LEU
Chi-restraints excluded: chain B residue  569 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  690 VAL
Chi-restraints excluded: chain B residue  701 THR
Chi-restraints excluded: chain B residue  723 THR
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  799 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 121 optimal weight:    5.9990
   chunk 8 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 171 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.084757 restraints weight = 22725.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.087487 restraints weight = 11512.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.089306 restraints weight = 6985.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.090517 restraints weight = 4770.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.091285 restraints weight = 3567.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.5937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10499  Z= 0.156
  Angle     :  0.673  11.703  14225  Z= 0.321
  Chirality :  0.041   0.185   1632
  Planarity :  0.005   0.057   1852
  Dihedral  :  7.712 175.998   1469
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.92 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.77 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.23), residues: 1301
  helix:  2.40 (0.20), residues: 678
  sheet: -0.39 (0.36), residues: 203
  loop : -0.59 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 194 
 TYR   0.020   0.001   TYR B 623 
 PHE   0.013   0.001   PHE B 725 
 TRP   0.032   0.003   TRP A 202 
 HIS   0.004   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10499)
  covalent geometry    : angle       0.67265 (14225)
  hydrogen bonds       : bond        0.03679 (  567)
  hydrogen bonds       : angle       4.38194 ( 1641)

===============================================================================
Job complete
usr+sys time: 1539.13 seconds
wall clock time: 27 minutes 20.49 seconds (1640.49 seconds total)