Starting phenix.real_space_refine
on Wed Sep 17 20:12:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ou2_13073/09_2025/7ou2_13073_neut.cif"
  }
  resolution = 4.8
  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=   0.022 sd=   0.074
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      54      5.16       5
     C    6781      2.51       5
     N    1916      2.21       5
     O    2043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10798
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 721, 5632
          Classifications: {'peptide': 721}
          Link IDs: {'PTRANS': 33, 'TRANS': 687}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 650, 5112
          Classifications: {'peptide': 650}
          Link IDs: {'PTRANS': 27, 'TRANS': 622}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.72, per 1000 atoms: 0.25
  Number of scatterers: 10798
  At special positions: 0
  Unit cell: (117.66, 99.64, 127.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       4     15.00
     O    2043      8.00
     N    1916      7.00
     C    6781      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: 1.03
  Conformation dependent library (CDL) restraints added in 498.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 10 sheets defined
      55.1% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 24
      removed outlier: 3.546A  pdb=" N   HIS A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 75 through 86
      removed outlier: 3.758A  pdb=" N   TYR A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 4.063A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 3.651A  pdb=" N   GLU A 203 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 218
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.650A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 266
    Processing helix  chain 'A' and resid 270 through 278
    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
      removed outlier: 3.687A  pdb=" N   LEU A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 344
      Proline residue:  A 340  - end of helix
      removed outlier: 3.744A  pdb=" N   GLN A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
    Processing helix  chain 'A' and resid 361 through 385
      Proline residue:  A 376  - end of helix
      removed outlier: 3.696A  pdb=" N   THR A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.987A  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 430 through 444
      removed outlier: 3.815A  pdb=" N   ALA A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 536
      removed outlier: 3.618A  pdb=" N   PHE A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 565
    Processing helix  chain 'A' and resid 585 through 592
    Processing helix  chain 'A' and resid 619 through 635
      removed outlier: 3.504A  pdb=" N   TYR A 623 " --> pdb=" O   GLY A 619 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   MET A 624 " --> pdb=" O   LYS A 620 " (cutoff:3.500A)
      removed outlier: 3.587A  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 731 through 733
      No H-bonds generated for 'chain 'A' and resid 731 through 733'
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 770 through 778
      removed outlier: 4.326A  pdb=" N   ALA A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
    Processing helix  chain 'B' and resid 18 through 24
      removed outlier: 3.615A  pdb=" N   HIS B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 51
    Processing helix  chain 'B' and resid 72 through 74
      No H-bonds generated for 'chain 'B' and resid 72 through 74'
    Processing helix  chain 'B' and resid 75 through 86
      removed outlier: 3.685A  pdb=" N   TYR B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 4.107A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 204
      removed outlier: 3.650A  pdb=" N   GLU B 203 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.664A  pdb=" N   ALA B 236 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 266
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.521A  pdb=" N   ARG B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 300 through 313
      removed outlier: 3.511A  pdb=" N   SER B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 333
      removed outlier: 3.711A  pdb=" N   LEU B 321 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 344
      Proline residue:  B 340  - end of helix
      removed outlier: 3.716A  pdb=" N   GLN B 344 " --> pdb=" O   PRO B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 357
    Processing helix  chain 'B' and resid 361 through 385
      Proline residue:  B 376  - end of helix
      removed outlier: 3.619A  pdb=" N   THR B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 521 through 536
    Processing helix  chain 'B' and resid 538 through 565
    Processing helix  chain 'B' and resid 587 through 591
    Processing helix  chain 'B' and resid 619 through 636
      removed outlier: 4.183A  pdb=" N   MET B 624 " --> pdb=" O   LYS B 620 " (cutoff:3.500A)
    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
    Processing helix  chain 'B' and resid 770 through 778
      removed outlier: 3.974A  pdb=" N   ALA B 774 " --> pdb=" O   SER B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 800
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.388A  pdb=" N   ILE A  66 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A  31 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   CYS A  93 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   PHE A  30 " --> pdb=" O   CYS A  93 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   GLN A  95 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 8.830A  pdb=" N   ARG A  32 " --> pdb=" O   GLN A  95 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   VAL A 110 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.614A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 9.171A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   ILE A 136 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269
      removed outlier: 6.926A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 8.415A  pdb=" N   THR A 655 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ARG A 652 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LEU A 691 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ASP A 693 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ARG A 656 " --> pdb=" O   ASP A 693 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 572
      removed outlier: 6.683A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A 644 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLU A 582 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   ASN A 599 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 609 through 613
      removed outlier: 6.798A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   THR A 613 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   ALA A 749 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP A 748 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER A 761 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU A 750 " --> pdb=" O   MET A 759 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   MET A 759 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   HIS A 752 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   ALA A 757 " --> pdb=" O   HIS A 752 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69
      removed outlier: 3.803A  pdb=" N   TYR B  31 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   PHE B  40 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   LEU B  29 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B  32 " --> pdb=" O   CYS B  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199
      removed outlier: 6.622A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR B 180 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 9.191A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   ILE B 136 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 269
      removed outlier: 6.791A  pdb=" N   ILE B 268 " --> pdb=" O   ILE B 653 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   THR B 655 " --> pdb=" O   ILE B 268 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ARG B 652 " --> pdb=" O   LEU B 689 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU B 691 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   MET B 692 " --> pdb=" O   LEU B 724 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 571 through 572
      removed outlier: 6.769A  pdb=" N   THR B 571 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS B 644 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 582 " --> pdb=" O   ASN B 599 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ASN B 599 " --> pdb=" O   GLU B 582 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 750 through 752

    552 hydrogen bonds defined for protein.
    1557 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: 1.34 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1839
        1.31 -     1.43: 2689
        1.43 -     1.56: 6346
        1.56 -     1.69: 6
        1.69 -     1.82: 96
  Bond restraints: 10976
  Sorted by residual:
  bond pdb=" C4  ADP A1801 "
       pdb=" C5  ADP A1801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.378  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C4  ADP B1801 "
       pdb=" C5  ADP B1801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" N   ARG A 199 "
       pdb=" CA  ARG A 199 "
    ideal  model  delta    sigma   weight residual
    1.453  1.495 -0.042 8.30e-03 1.45e+04 2.51e+01
  bond pdb=" N   ARG B 199 "
       pdb=" CA  ARG B 199 "
    ideal  model  delta    sigma   weight residual
    1.453  1.493 -0.040 8.30e-03 1.45e+04 2.30e+01
  bond pdb=" C   PRO B 615 "
       pdb=" O   PRO B 615 "
    ideal  model  delta    sigma   weight residual
    1.233  1.177  0.056 1.19e-02 7.06e+03 2.21e+01
  ... (remaining 10971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 12295
        2.51 -     5.03: 2462
        5.03 -     7.54: 88
        7.54 -    10.05: 23
       10.05 -    12.56: 1
  Bond angle restraints: 14869
  Sorted by residual:
  angle pdb=" N   CYS B 297 "
        pdb=" CA  CYS B 297 "
        pdb=" C   CYS B 297 "
      ideal   model   delta    sigma   weight residual
     111.56  101.89    9.67 1.38e+00 5.25e-01 4.91e+01
  angle pdb=" N   CYS A 297 "
        pdb=" CA  CYS A 297 "
        pdb=" C   CYS A 297 "
      ideal   model   delta    sigma   weight residual
     111.71  102.87    8.84 1.34e+00 5.57e-01 4.35e+01
  angle pdb=" C   THR B 669 "
        pdb=" CA  THR B 669 "
        pdb=" CB  THR B 669 "
      ideal   model   delta    sigma   weight residual
     110.88  101.06    9.82 1.57e+00 4.06e-01 3.91e+01
  angle pdb=" N   ARG A 697 "
        pdb=" CA  ARG A 697 "
        pdb=" C   ARG A 697 "
      ideal   model   delta    sigma   weight residual
     112.93  106.08    6.85 1.12e+00 7.97e-01 3.74e+01
  angle pdb=" N   ILE A 636 "
        pdb=" CA  ILE A 636 "
        pdb=" C   ILE A 636 "
      ideal   model   delta    sigma   weight residual
     112.80  105.92    6.88 1.15e+00 7.56e-01 3.58e+01
  ... (remaining 14864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.73: 6456
       26.73 -    53.45: 244
       53.45 -    80.18: 26
       80.18 -   106.91: 3
      106.91 -   133.63: 3
  Dihedral angle restraints: 6732
    sinusoidal: 2754
      harmonic: 3978
  Sorted by residual:
  dihedral pdb=" O2A ADP A1801 "
           pdb=" O3A ADP A1801 "
           pdb=" PA  ADP A1801 "
           pdb=" PB  ADP A1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   73.64 -133.63     1      2.00e+01 2.50e-03 4.06e+01
  dihedral pdb=" O2A ADP B1801 "
           pdb=" O3A ADP B1801 "
           pdb=" PA  ADP B1801 "
           pdb=" PB  ADP B1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   60.77 -120.77     1      2.00e+01 2.50e-03 3.63e+01
  dihedral pdb=" O1B ADP B1801 "
           pdb=" O3A ADP B1801 "
           pdb=" PB  ADP B1801 "
           pdb=" PA  ADP B1801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  179.79  120.21     1      2.00e+01 2.50e-03 3.61e+01
  ... (remaining 6729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 768
       0.081 -    0.163: 641
       0.163 -    0.244: 252
       0.244 -    0.325: 42
       0.325 -    0.406: 3
  Chirality restraints: 1706
  Sorted by residual:
  chirality pdb=" CA  TYR B 528 "
            pdb=" N   TYR B 528 "
            pdb=" C   TYR B 528 "
            pdb=" CB  TYR B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CA  TYR B 635 "
            pdb=" N   TYR B 635 "
            pdb=" C   TYR B 635 "
            pdb=" CB  TYR B 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.83e+00
  chirality pdb=" CA  TYR A 635 "
            pdb=" N   TYR A 635 "
            pdb=" C   TYR A 635 "
            pdb=" CB  TYR A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  ... (remaining 1703 not shown)

  Planarity restraints: 1934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 275 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   ARG B 275 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ARG B 275 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASN B 276 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 642 "   -0.016 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   ALA B 642 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ALA B 642 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN B 643 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 378 "   -0.015 2.00e-02 2.50e+03   3.09e-02 9.53e+00
        pdb=" C   LEU A 378 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LEU A 378 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 379 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1931 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 4421
        2.95 -     3.44: 11219
        3.44 -     3.93: 18368
        3.93 -     4.41: 20845
        4.41 -     4.90: 33099
  Nonbonded interactions: 87952
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 139 "
            pdb=" O   ASP A 139 "
     model   vdw
     2.465 2.496
  nonbonded pdb=" N   VAL B 781 "
            pdb=" O   VAL B 781 "
     model   vdw
     2.473 2.496
  nonbonded pdb=" N   VAL A 781 "
            pdb=" O   VAL A 781 "
     model   vdw
     2.486 2.496
  nonbonded pdb=" N   ASP B 139 "
            pdb=" O   ASP B 139 "
     model   vdw
     2.489 2.496
  nonbonded pdb=" N   THR A  56 "
            pdb=" O   THR A  56 "
     model   vdw
     2.510 2.496
  ... (remaining 87947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 17 through 56 or resid 67 through 94 or resid 109 through  \ 
412 or resid 520 through 1801))
  selection = (chain 'B' and (resid 17 through 662 or resid 667 through 1801))
}

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:             0.110
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.520
  Find NCS groups from input model:        0.330
  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:1.270
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6411
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   0.112  10976  Z= 0.995
  Angle     :  1.801  12.564  14869  Z= 1.382
  Chirality :  0.120   0.406   1706
  Planarity :  0.008   0.034   1934
  Dihedral  : 14.072 133.634   4156
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.21), residues: 1355
  helix:  2.66 (0.18), residues: 649
  sheet: -0.52 (0.37), residues: 148
  loop : -0.55 (0.23), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG A 420 
 TYR   0.037   0.005   TYR B 528 
 PHE   0.021   0.004   PHE A 730 
 TRP   0.026   0.004   TRP A 137 
 HIS   0.007   0.002   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.01308 (10976)
  covalent geometry    : angle       1.80104 (14869)
  hydrogen bonds       : bond        0.21782 (  552)
  hydrogen bonds       : angle       6.80673 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 365
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9234 (m) cc_final: 0.8768 (p)
REVERT: A  260 MET cc_start: 0.6887 (tpt) cc_final: 0.6471 (tpp)
REVERT: A  323 GLU cc_start: 0.8661 (tt0) cc_final: 0.8196 (tm-30)
REVERT: A  365 LEU cc_start: 0.8581 (mt) cc_final: 0.7161 (mt)
REVERT: A  441 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (p0)
REVERT: A  528 TYR cc_start: 0.6743 (t80) cc_final: 0.6098 (t80)
REVERT: A  552 LEU cc_start: 0.9147 (tp) cc_final: 0.8843 (mp)
REVERT: A  615 PRO cc_start: 0.6031 (Cg_endo) cc_final: 0.3607 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8204 (mmm) cc_final: 0.7295 (mmt)
REVERT: A  740 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8134 (pm20)
REVERT: B   73 TYR cc_start: 0.5483 (p90) cc_final: 0.5127 (p90)
REVERT: B  157 LEU cc_start: 0.7350 (tp) cc_final: 0.6803 (pp)
REVERT: B  158 SER cc_start: 0.5808 (p) cc_final: 0.5407 (t)
REVERT: B  173 THR cc_start: 0.7410 (p) cc_final: 0.6974 (t)
REVERT: B  333 ASP cc_start: 0.8353 (m-30) cc_final: 0.7833 (t0)
REVERT: B  368 MET cc_start: 0.7736 (ttm) cc_final: 0.7527 (ttm)
REVERT: B  524 GLU cc_start: 0.7075 (pt0) cc_final: 0.6849 (mm-30)
REVERT: B  602 ASN cc_start: 0.7724 (m-40) cc_final: 0.7449 (m-40)
REVERT: B  687 TYR cc_start: 0.7565 (m-80) cc_final: 0.7021 (m-80)
REVERT: B  718 LYS cc_start: 0.7581 (mttp) cc_final: 0.7194 (tmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1512
  time to fit residues: 71.0303
Evaluate side-chains
  236 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   30.0000
   chunk 55 optimal weight:    5.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
A 326 GLN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 ASN
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 683 ASN
B 171 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.076181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.067095 restraints weight = 76732.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.068542 restraints weight = 56175.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.069643 restraints weight = 42896.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.070445 restraints weight = 33861.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.071132 restraints weight = 27826.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  10976  Z= 0.212
  Angle     :  0.792  10.681  14869  Z= 0.408
  Chirality :  0.046   0.180   1706
  Planarity :  0.007   0.075   1934
  Dihedral  :  7.444 121.319   1532
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.87 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.21), residues: 1355
  helix:  1.39 (0.19), residues: 664
  sheet: -0.50 (0.34), residues: 175
  loop : -0.69 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 172 
 TYR   0.034   0.003   TYR B 528 
 PHE   0.032   0.003   PHE B 155 
 TRP   0.016   0.002   TRP B 709 
 HIS   0.009   0.002   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (10976)
  covalent geometry    : angle       0.79242 (14869)
  hydrogen bonds       : bond        0.04875 (  552)
  hydrogen bonds       : angle       5.17126 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 268
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.7250 (mttp) cc_final: 0.6992 (mttp)
REVERT: A   83 LEU cc_start: 0.7747 (mt) cc_final: 0.7518 (mt)
REVERT: A  133 LEU cc_start: 0.7932 (tp) cc_final: 0.7435 (tp)
REVERT: A  157 LEU cc_start: 0.8097 (tt) cc_final: 0.7814 (tt)
REVERT: A  222 LEU cc_start: 0.7960 (mt) cc_final: 0.7672 (pt)
REVERT: A  229 ASN cc_start: 0.8795 (t0) cc_final: 0.8506 (t0)
REVERT: A  258 ILE cc_start: 0.7654 (tt) cc_final: 0.7258 (tt)
REVERT: A  260 MET cc_start: 0.6366 (tpt) cc_final: 0.6138 (tpp)
REVERT: A  297 CYS cc_start: 0.5656 (m) cc_final: 0.5332 (m)
REVERT: A  323 GLU cc_start: 0.8503 (tt0) cc_final: 0.8150 (tm-30)
REVERT: A  365 LEU cc_start: 0.8621 (mt) cc_final: 0.7756 (mt)
REVERT: A  382 LEU cc_start: 0.8417 (mt) cc_final: 0.7924 (mt)
REVERT: A  397 MET cc_start: 0.8384 (mtm) cc_final: 0.7898 (mtt)
REVERT: A  441 ASP cc_start: 0.8981 (m-30) cc_final: 0.8576 (p0)
REVERT: A  528 TYR cc_start: 0.7067 (t80) cc_final: 0.6778 (t80)
REVERT: A  617 MET cc_start: 0.8242 (mmm) cc_final: 0.7728 (mmt)
REVERT: B   20 LEU cc_start: 0.9150 (tp) cc_final: 0.8794 (tp)
REVERT: B  155 PHE cc_start: 0.6400 (t80) cc_final: 0.6057 (t80)
REVERT: B  524 GLU cc_start: 0.7717 (pt0) cc_final: 0.5948 (mm-30)
REVERT: B  526 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6378 (pm20)
REVERT: B  529 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8364 (tm-30)
REVERT: B  533 ASP cc_start: 0.7773 (m-30) cc_final: 0.7486 (m-30)
REVERT: B  579 ARG cc_start: 0.6762 (tmm160) cc_final: 0.6376 (ttp80)
REVERT: B  602 ASN cc_start: 0.7838 (m-40) cc_final: 0.7591 (p0)
REVERT: B  617 MET cc_start: 0.7351 (mmt) cc_final: 0.6469 (mmm)
REVERT: B  624 MET cc_start: 0.8608 (tmm) cc_final: 0.7972 (ptm)
REVERT: B  644 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7157 (ptmm)
REVERT: B  759 MET cc_start: 0.8455 (mmp) cc_final: 0.8207 (mmp)
REVERT: B  795 GLU cc_start: 0.8801 (pt0) cc_final: 0.8549 (pp20)
  outliers start: 5
  outliers final: 1
  residues processed: 273
  average time/residue: 0.1471
  time to fit residues: 52.4611
Evaluate side-chains
  205 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 203
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 1 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 57 optimal weight:   30.0000
   chunk 59 optimal weight:    5.9990
   chunk 119 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 82 optimal weight:   30.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS
A 326 GLN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN
** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 760 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.074695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.065559 restraints weight = 69457.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.067091 restraints weight = 49857.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.068254 restraints weight = 37551.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.069143 restraints weight = 29435.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.069837 restraints weight = 23791.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10976  Z= 0.159
  Angle     :  0.702   7.466  14869  Z= 0.354
  Chirality :  0.043   0.164   1706
  Planarity :  0.006   0.064   1934
  Dihedral  :  7.140 122.224   1532
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.82 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.21), residues: 1355
  helix:  1.35 (0.19), residues: 665
  sheet: -0.44 (0.34), residues: 186
  loop : -0.77 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 404 
 TYR   0.033   0.002   TYR B  31 
 PHE   0.021   0.002   PHE B 334 
 TRP   0.014   0.002   TRP B 709 
 HIS   0.004   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10976)
  covalent geometry    : angle       0.70182 (14869)
  hydrogen bonds       : bond        0.04191 (  552)
  hydrogen bonds       : angle       4.97051 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 240
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.6359 (m-10) cc_final: 0.6078 (m-80)
REVERT: A  128 ARG cc_start: 0.5689 (ttt180) cc_final: 0.5410 (ttt180)
REVERT: A  143 PHE cc_start: 0.6193 (m-80) cc_final: 0.5876 (m-80)
REVERT: A  206 ILE cc_start: 0.9113 (tp) cc_final: 0.8889 (mp)
REVERT: A  207 ASP cc_start: 0.8950 (m-30) cc_final: 0.8662 (m-30)
REVERT: A  222 LEU cc_start: 0.8079 (mt) cc_final: 0.7724 (pt)
REVERT: A  229 ASN cc_start: 0.8951 (t0) cc_final: 0.8619 (t0)
REVERT: A  323 GLU cc_start: 0.8441 (tt0) cc_final: 0.8061 (tm-30)
REVERT: A  441 ASP cc_start: 0.8913 (m-30) cc_final: 0.8617 (p0)
REVERT: A  528 TYR cc_start: 0.6970 (t80) cc_final: 0.6765 (t80)
REVERT: A  552 LEU cc_start: 0.8861 (mt) cc_final: 0.8638 (mp)
REVERT: A  615 PRO cc_start: 0.6966 (Cg_endo) cc_final: 0.5537 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8204 (mmm) cc_final: 0.7803 (mmm)
REVERT: A  692 MET cc_start: 0.8057 (mmp) cc_final: 0.7728 (mmp)
REVERT: B  174 ASN cc_start: 0.8594 (t0) cc_final: 0.8249 (t0)
REVERT: B  269 MET cc_start: 0.8520 (mtp) cc_final: 0.8254 (mtm)
REVERT: B  288 GLU cc_start: 0.8342 (mp0) cc_final: 0.8127 (mp0)
REVERT: B  289 ASN cc_start: 0.8668 (t0) cc_final: 0.8462 (t0)
REVERT: B  529 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8173 (tm-30)
REVERT: B  533 ASP cc_start: 0.7747 (m-30) cc_final: 0.7438 (m-30)
REVERT: B  552 LEU cc_start: 0.8761 (mm) cc_final: 0.8520 (mm)
REVERT: B  644 LYS cc_start: 0.8095 (tmtt) cc_final: 0.6687 (tptt)
REVERT: B  654 PHE cc_start: 0.4660 (m-80) cc_final: 0.4325 (m-80)
REVERT: B  692 MET cc_start: 0.5692 (ttp) cc_final: 0.5476 (ttp)
REVERT: B  759 MET cc_start: 0.8335 (mmp) cc_final: 0.8132 (mmm)
  outliers start: 4
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1311
  time to fit residues: 42.6823
Evaluate side-chains
  189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 102 optimal weight:    0.0170
   chunk 22 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0370
   overall best weight:    2.2102

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

Flipped N/Q/H residues before XYZ refinement:
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 HIS
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
B 276 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 746 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.076235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.067017 restraints weight = 76751.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.068496 restraints weight = 55858.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.069611 restraints weight = 42662.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.070469 restraints weight = 33987.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.071153 restraints weight = 27828.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10976  Z= 0.139
  Angle     :  0.685  10.103  14869  Z= 0.346
  Chirality :  0.043   0.187   1706
  Planarity :  0.006   0.081   1934
  Dihedral  :  6.808 120.102   1532
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.43 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.22), residues: 1355
  helix:  1.45 (0.19), residues: 657
  sheet: -0.22 (0.37), residues: 167
  loop : -0.76 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 363 
 TYR   0.021   0.002   TYR B  31 
 PHE   0.018   0.001   PHE A 670 
 TRP   0.023   0.002   TRP A 709 
 HIS   0.008   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10976)
  covalent geometry    : angle       0.68509 (14869)
  hydrogen bonds       : bond        0.04044 (  552)
  hydrogen bonds       : angle       4.86489 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.6057 (m-10) cc_final: 0.5742 (m-80)
REVERT: A  143 PHE cc_start: 0.6013 (m-80) cc_final: 0.5573 (m-80)
REVERT: A  170 LEU cc_start: 0.7497 (mt) cc_final: 0.7214 (mt)
REVERT: A  201 LEU cc_start: 0.7717 (tp) cc_final: 0.7481 (tp)
REVERT: A  206 ILE cc_start: 0.9113 (tp) cc_final: 0.8623 (mp)
REVERT: A  207 ASP cc_start: 0.8968 (m-30) cc_final: 0.8742 (m-30)
REVERT: A  222 LEU cc_start: 0.8254 (mt) cc_final: 0.7833 (pt)
REVERT: A  229 ASN cc_start: 0.8950 (t0) cc_final: 0.8551 (t0)
REVERT: A  374 GLN cc_start: 0.7638 (tp40) cc_final: 0.7299 (tt0)
REVERT: A  432 GLU cc_start: 0.8603 (tt0) cc_final: 0.8009 (tp30)
REVERT: A  441 ASP cc_start: 0.9008 (m-30) cc_final: 0.8558 (p0)
REVERT: A  615 PRO cc_start: 0.7235 (Cg_endo) cc_final: 0.5826 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8269 (mmm) cc_final: 0.7815 (mmt)
REVERT: B  174 ASN cc_start: 0.8679 (t0) cc_final: 0.8330 (t0)
REVERT: B  288 GLU cc_start: 0.8378 (mp0) cc_final: 0.7954 (mp0)
REVERT: B  289 ASN cc_start: 0.8491 (t0) cc_final: 0.7895 (t0)
REVERT: B  524 GLU cc_start: 0.8062 (pt0) cc_final: 0.7232 (mm-30)
REVERT: B  529 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8168 (tm-30)
REVERT: B  533 ASP cc_start: 0.7825 (m-30) cc_final: 0.7497 (m-30)
REVERT: B  552 LEU cc_start: 0.8686 (mm) cc_final: 0.8466 (mm)
REVERT: B  579 ARG cc_start: 0.6393 (tmm160) cc_final: 0.5939 (ttp80)
REVERT: B  692 MET cc_start: 0.5636 (ttp) cc_final: 0.3952 (ttm)
REVERT: B  717 ASN cc_start: 0.8402 (t0) cc_final: 0.8167 (t0)
REVERT: B  759 MET cc_start: 0.8392 (mmp) cc_final: 0.8093 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 230
  average time/residue: 0.1212
  time to fit residues: 37.1514
Evaluate side-chains
  183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 136 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 109 optimal weight:   20.0000
   chunk 123 optimal weight:   30.0000
   chunk 48 optimal weight:   10.0000
   chunk 135 optimal weight:   30.0000
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 ASN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
A 626 GLN
A 734 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.073148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.064163 restraints weight = 70250.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.065676 restraints weight = 49830.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.066788 restraints weight = 37277.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.067689 restraints weight = 29199.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.068325 restraints weight = 23481.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.6116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10976  Z= 0.171
  Angle     :  0.722  10.226  14869  Z= 0.369
  Chirality :  0.043   0.181   1706
  Planarity :  0.005   0.069   1934
  Dihedral  :  6.653 118.553   1532
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.22), residues: 1355
  helix:  1.34 (0.19), residues: 658
  sheet: -0.31 (0.39), residues: 152
  loop : -0.94 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 163 
 TYR   0.020   0.002   TYR A 635 
 PHE   0.015   0.002   PHE B 725 
 TRP   0.022   0.003   TRP B 709 
 HIS   0.006   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10976)
  covalent geometry    : angle       0.72173 (14869)
  hydrogen bonds       : bond        0.03877 (  552)
  hydrogen bonds       : angle       4.88914 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.6372 (m-10) cc_final: 0.6146 (m-80)
REVERT: A  143 PHE cc_start: 0.6170 (m-80) cc_final: 0.5899 (m-80)
REVERT: A  166 MET cc_start: 0.6391 (tpt) cc_final: 0.5966 (tpt)
REVERT: A  170 LEU cc_start: 0.7644 (mt) cc_final: 0.7342 (mt)
REVERT: A  222 LEU cc_start: 0.8227 (mt) cc_final: 0.7831 (pt)
REVERT: A  229 ASN cc_start: 0.8968 (t0) cc_final: 0.8514 (t0)
REVERT: A  381 GLN cc_start: 0.8467 (mt0) cc_final: 0.8233 (mt0)
REVERT: A  432 GLU cc_start: 0.8609 (tt0) cc_final: 0.7872 (tp30)
REVERT: A  441 ASP cc_start: 0.9003 (m-30) cc_final: 0.8520 (p0)
REVERT: A  528 TYR cc_start: 0.7171 (t80) cc_final: 0.6342 (t80)
REVERT: A  615 PRO cc_start: 0.7242 (Cg_endo) cc_final: 0.5932 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8077 (mmm) cc_final: 0.7746 (mmt)
REVERT: A  784 GLU cc_start: 0.8937 (pm20) cc_final: 0.8679 (pm20)
REVERT: B  155 PHE cc_start: 0.6626 (t80) cc_final: 0.5913 (t80)
REVERT: B  189 LEU cc_start: 0.8760 (mm) cc_final: 0.8440 (mt)
REVERT: B  258 ILE cc_start: 0.9079 (tt) cc_final: 0.8527 (tt)
REVERT: B  288 GLU cc_start: 0.8474 (mp0) cc_final: 0.8048 (mp0)
REVERT: B  289 ASN cc_start: 0.8553 (t0) cc_final: 0.7874 (t0)
REVERT: B  524 GLU cc_start: 0.7881 (pt0) cc_final: 0.6369 (mm-30)
REVERT: B  529 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8189 (tm-30)
REVERT: B  533 ASP cc_start: 0.7662 (m-30) cc_final: 0.7318 (m-30)
REVERT: B  610 LEU cc_start: 0.9088 (pt) cc_final: 0.8430 (mp)
REVERT: B  624 MET cc_start: 0.8620 (tmm) cc_final: 0.7917 (mtp)
REVERT: B  644 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8206 (ptmm)
REVERT: B  717 ASN cc_start: 0.8308 (t0) cc_final: 0.7996 (t0)
REVERT: B  724 LEU cc_start: 0.8465 (tp) cc_final: 0.7432 (tp)
REVERT: B  725 PHE cc_start: 0.7272 (m-80) cc_final: 0.7062 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1245
  time to fit residues: 36.3138
Evaluate side-chains
  173 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 4 optimal weight:   30.0000
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 131 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 118 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.072597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.063658 restraints weight = 71777.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.065146 restraints weight = 51460.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.066258 restraints weight = 38746.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.067117 restraints weight = 30402.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.067773 restraints weight = 24568.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.6458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10976  Z= 0.173
  Angle     :  0.743  10.527  14869  Z= 0.372
  Chirality :  0.044   0.210   1706
  Planarity :  0.006   0.108   1934
  Dihedral  :  6.670 118.821   1532
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 19.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.29 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.22), residues: 1355
  helix:  1.33 (0.19), residues: 654
  sheet: -0.34 (0.39), residues: 164
  loop : -0.97 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  19 
 TYR   0.037   0.002   TYR B  31 
 PHE   0.018   0.002   PHE A  30 
 TRP   0.025   0.002   TRP B 709 
 HIS   0.006   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10976)
  covalent geometry    : angle       0.74297 (14869)
  hydrogen bonds       : bond        0.03884 (  552)
  hydrogen bonds       : angle       4.92628 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 210
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 PHE cc_start: 0.6407 (m-10) cc_final: 0.6155 (m-80)
REVERT: A  113 ILE cc_start: 0.7794 (mp) cc_final: 0.7589 (mm)
REVERT: A  143 PHE cc_start: 0.6114 (m-80) cc_final: 0.5825 (m-80)
REVERT: A  166 MET cc_start: 0.6344 (tpt) cc_final: 0.5691 (tpt)
REVERT: A  172 ARG cc_start: 0.6656 (mtt180) cc_final: 0.5990 (mtp180)
REVERT: A  222 LEU cc_start: 0.8138 (mt) cc_final: 0.7760 (pt)
REVERT: A  229 ASN cc_start: 0.8980 (t0) cc_final: 0.8536 (t0)
REVERT: A  381 GLN cc_start: 0.8622 (mt0) cc_final: 0.8421 (mt0)
REVERT: A  432 GLU cc_start: 0.8598 (tt0) cc_final: 0.7859 (tp30)
REVERT: A  441 ASP cc_start: 0.8986 (m-30) cc_final: 0.8593 (p0)
REVERT: A  528 TYR cc_start: 0.7308 (t80) cc_final: 0.6494 (t80)
REVERT: A  582 GLU cc_start: 0.7595 (pm20) cc_final: 0.7372 (mp0)
REVERT: A  615 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.5941 (Cg_exo)
REVERT: A  617 MET cc_start: 0.8020 (mmm) cc_final: 0.7704 (mmt)
REVERT: B  155 PHE cc_start: 0.6744 (t80) cc_final: 0.5978 (t80)
REVERT: B  174 ASN cc_start: 0.8428 (t0) cc_final: 0.8015 (t0)
REVERT: B  258 ILE cc_start: 0.9085 (tt) cc_final: 0.8572 (tt)
REVERT: B  288 GLU cc_start: 0.8551 (mp0) cc_final: 0.8128 (mp0)
REVERT: B  289 ASN cc_start: 0.8572 (t0) cc_final: 0.7947 (t0)
REVERT: B  529 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8219 (tm-30)
REVERT: B  533 ASP cc_start: 0.7669 (m-30) cc_final: 0.7296 (m-30)
REVERT: B  610 LEU cc_start: 0.9152 (pt) cc_final: 0.8636 (mp)
REVERT: B  717 ASN cc_start: 0.8364 (t0) cc_final: 0.8062 (t0)
REVERT: B  752 HIS cc_start: 0.8215 (p-80) cc_final: 0.8014 (p-80)
  outliers start: 2
  outliers final: 0
  residues processed: 211
  average time/residue: 0.1369
  time to fit residues: 38.6792
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.071735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.063033 restraints weight = 71117.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.064474 restraints weight = 50986.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.065559 restraints weight = 38455.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.066389 restraints weight = 30209.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.066990 restraints weight = 24484.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.6750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10976  Z= 0.174
  Angle     :  0.743   8.751  14869  Z= 0.375
  Chirality :  0.044   0.164   1706
  Planarity :  0.005   0.050   1934
  Dihedral  :  6.639 118.855   1532
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.22), residues: 1355
  helix:  1.28 (0.19), residues: 651
  sheet: -0.36 (0.40), residues: 153
  loop : -1.08 (0.24), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 249 
 TYR   0.029   0.002   TYR B  31 
 PHE   0.016   0.002   PHE B 654 
 TRP   0.025   0.002   TRP B 709 
 HIS   0.004   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10976)
  covalent geometry    : angle       0.74288 (14869)
  hydrogen bonds       : bond        0.03795 (  552)
  hydrogen bonds       : angle       5.07429 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 LEU cc_start: 0.7917 (tp) cc_final: 0.7135 (tp)
REVERT: A  143 PHE cc_start: 0.5973 (m-80) cc_final: 0.5718 (m-80)
REVERT: A  170 LEU cc_start: 0.7724 (mt) cc_final: 0.7397 (mt)
REVERT: A  222 LEU cc_start: 0.8425 (mt) cc_final: 0.8050 (pt)
REVERT: A  229 ASN cc_start: 0.8935 (t0) cc_final: 0.8584 (t0)
REVERT: A  432 GLU cc_start: 0.8558 (tt0) cc_final: 0.7867 (tp30)
REVERT: A  441 ASP cc_start: 0.8979 (m-30) cc_final: 0.8570 (p0)
REVERT: A  528 TYR cc_start: 0.7368 (t80) cc_final: 0.6529 (t80)
REVERT: A  615 PRO cc_start: 0.7254 (Cg_endo) cc_final: 0.5958 (Cg_exo)
REVERT: A  617 MET cc_start: 0.7959 (mmm) cc_final: 0.7733 (mmt)
REVERT: A  784 GLU cc_start: 0.8858 (pm20) cc_final: 0.8641 (pm20)
REVERT: B  155 PHE cc_start: 0.6810 (t80) cc_final: 0.6597 (t80)
REVERT: B  288 GLU cc_start: 0.8603 (mp0) cc_final: 0.8228 (mp0)
REVERT: B  289 ASN cc_start: 0.8623 (t0) cc_final: 0.8051 (t0)
REVERT: B  386 ASP cc_start: 0.7448 (p0) cc_final: 0.7221 (p0)
REVERT: B  524 GLU cc_start: 0.8058 (pt0) cc_final: 0.6513 (mm-30)
REVERT: B  529 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8217 (tm-30)
REVERT: B  533 ASP cc_start: 0.7656 (m-30) cc_final: 0.7306 (m-30)
REVERT: B  624 MET cc_start: 0.8575 (tmm) cc_final: 0.7952 (mtp)
REVERT: B  692 MET cc_start: 0.3792 (ttt) cc_final: 0.3087 (ttt)
REVERT: B  717 ASN cc_start: 0.8270 (t0) cc_final: 0.7479 (t0)
REVERT: B  725 PHE cc_start: 0.7541 (m-80) cc_final: 0.5468 (m-80)
REVERT: B  739 MET cc_start: 0.6027 (ttt) cc_final: 0.5722 (ttt)
REVERT: B  752 HIS cc_start: 0.8328 (p-80) cc_final: 0.8101 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1374
  time to fit residues: 37.4627
Evaluate side-chains
  164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 3 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 105 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    4.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 GLN
A 557 ASN
B 131 ASN
B 212 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.071159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.062537 restraints weight = 71371.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.063992 restraints weight = 51120.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.065098 restraints weight = 38495.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.065931 restraints weight = 30133.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.066578 restraints weight = 24359.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.7051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10976  Z= 0.173
  Angle     :  0.724   8.667  14869  Z= 0.366
  Chirality :  0.043   0.173   1706
  Planarity :  0.005   0.047   1934
  Dihedral  :  6.570 119.035   1532
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.88 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.22), residues: 1355
  helix:  1.29 (0.20), residues: 646
  sheet: -0.48 (0.39), residues: 162
  loop : -1.07 (0.24), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 232 
 TYR   0.023   0.002   TYR B  31 
 PHE   0.015   0.002   PHE B 670 
 TRP   0.023   0.002   TRP B 709 
 HIS   0.004   0.001   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10976)
  covalent geometry    : angle       0.72380 (14869)
  hydrogen bonds       : bond        0.03756 (  552)
  hydrogen bonds       : angle       5.08236 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 LEU cc_start: 0.7924 (tp) cc_final: 0.7553 (tp)
REVERT: A  143 PHE cc_start: 0.6225 (m-80) cc_final: 0.5839 (m-10)
REVERT: A  222 LEU cc_start: 0.8435 (mt) cc_final: 0.7987 (pt)
REVERT: A  229 ASN cc_start: 0.9005 (t0) cc_final: 0.8633 (t0)
REVERT: A  432 GLU cc_start: 0.8523 (tt0) cc_final: 0.7838 (tp30)
REVERT: A  441 ASP cc_start: 0.8948 (m-30) cc_final: 0.8522 (p0)
REVERT: A  552 LEU cc_start: 0.8981 (mm) cc_final: 0.8722 (mp)
REVERT: A  615 PRO cc_start: 0.7287 (Cg_endo) cc_final: 0.6003 (Cg_exo)
REVERT: A  784 GLU cc_start: 0.8827 (pm20) cc_final: 0.8594 (pm20)
REVERT: B   73 TYR cc_start: 0.6610 (p90) cc_final: 0.6083 (p90)
REVERT: B  386 ASP cc_start: 0.7357 (p0) cc_final: 0.7100 (p0)
REVERT: B  524 GLU cc_start: 0.7991 (pt0) cc_final: 0.6442 (mm-30)
REVERT: B  529 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8211 (tm-30)
REVERT: B  533 ASP cc_start: 0.7726 (m-30) cc_final: 0.7374 (m-30)
REVERT: B  543 GLN cc_start: 0.6622 (mt0) cc_final: 0.5805 (mm110)
REVERT: B  624 MET cc_start: 0.8331 (tmm) cc_final: 0.8041 (mtp)
REVERT: B  644 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8309 (ptmm)
REVERT: B  692 MET cc_start: 0.4301 (ttt) cc_final: 0.3899 (ttt)
REVERT: B  717 ASN cc_start: 0.8162 (t0) cc_final: 0.7391 (t0)
REVERT: B  725 PHE cc_start: 0.7362 (m-80) cc_final: 0.5580 (m-80)
REVERT: B  739 MET cc_start: 0.6166 (ttt) cc_final: 0.5901 (ttt)
REVERT: B  752 HIS cc_start: 0.8394 (p-80) cc_final: 0.8096 (p-80)
REVERT: B  795 GLU cc_start: 0.8585 (mp0) cc_final: 0.8373 (pm20)
  outliers start: 2
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1265
  time to fit residues: 33.4216
Evaluate side-chains
  164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 134 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 129 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 83 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 115 optimal weight:   50.0000
   overall best weight:    8.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 602 ASN
B 734 GLN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.068959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.060563 restraints weight = 71577.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.061982 restraints weight = 51234.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.063043 restraints weight = 38497.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.063863 restraints weight = 30164.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.064489 restraints weight = 24308.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.7479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10976  Z= 0.233
  Angle     :  0.800   8.544  14869  Z= 0.407
  Chirality :  0.046   0.218   1706
  Planarity :  0.006   0.055   1934
  Dihedral  :  6.820 120.202   1532
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 25.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.44 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.22), residues: 1355
  helix:  0.90 (0.20), residues: 641
  sheet: -0.35 (0.40), residues: 160
  loop : -1.24 (0.24), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 172 
 TYR   0.026   0.003   TYR A 635 
 PHE   0.017   0.002   PHE B 654 
 TRP   0.032   0.003   TRP B 709 
 HIS   0.006   0.001   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (10976)
  covalent geometry    : angle       0.79992 (14869)
  hydrogen bonds       : bond        0.04114 (  552)
  hydrogen bonds       : angle       5.32921 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.6451 (m-80) cc_final: 0.6102 (m-10)
REVERT: A  222 LEU cc_start: 0.8393 (mt) cc_final: 0.8085 (pt)
REVERT: A  229 ASN cc_start: 0.9079 (t0) cc_final: 0.8714 (t0)
REVERT: A  382 LEU cc_start: 0.7974 (mt) cc_final: 0.7649 (tp)
REVERT: A  432 GLU cc_start: 0.8596 (tt0) cc_final: 0.7897 (tp30)
REVERT: A  441 ASP cc_start: 0.8980 (m-30) cc_final: 0.8549 (p0)
REVERT: A  552 LEU cc_start: 0.8942 (mm) cc_final: 0.8700 (mp)
REVERT: A  615 PRO cc_start: 0.7458 (Cg_endo) cc_final: 0.6341 (Cg_exo)
REVERT: A  784 GLU cc_start: 0.8843 (pm20) cc_final: 0.8577 (pm20)
REVERT: B   17 TYR cc_start: 0.3829 (t80) cc_final: 0.3294 (t80)
REVERT: B   73 TYR cc_start: 0.6870 (p90) cc_final: 0.6369 (p90)
REVERT: B  288 GLU cc_start: 0.8571 (pm20) cc_final: 0.8348 (pm20)
REVERT: B  386 ASP cc_start: 0.7125 (p0) cc_final: 0.6827 (p0)
REVERT: B  543 GLN cc_start: 0.6676 (mt0) cc_final: 0.5860 (mm110)
REVERT: B  644 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8153 (tptp)
REVERT: B  692 MET cc_start: 0.4849 (ttt) cc_final: 0.4309 (ttt)
REVERT: B  717 ASN cc_start: 0.8134 (t0) cc_final: 0.7292 (t0)
REVERT: B  725 PHE cc_start: 0.6949 (m-80) cc_final: 0.5577 (m-80)
REVERT: B  739 MET cc_start: 0.6487 (ttt) cc_final: 0.6117 (ttt)
REVERT: B  752 HIS cc_start: 0.8455 (p-80) cc_final: 0.8198 (p-80)
REVERT: B  795 GLU cc_start: 0.8895 (mp0) cc_final: 0.8207 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1290
  time to fit residues: 34.8332
Evaluate side-chains
  164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 118 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 64 optimal weight:   20.0000
   chunk 66 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 ASN
B 602 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.069821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.061283 restraints weight = 70946.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.062744 restraints weight = 50732.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.063836 restraints weight = 38168.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.064684 restraints weight = 29813.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.065316 restraints weight = 23973.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.7665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10976  Z= 0.175
  Angle     :  0.768  10.202  14869  Z= 0.388
  Chirality :  0.045   0.192   1706
  Planarity :  0.005   0.060   1934
  Dihedral  :  6.759 119.701   1532
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 22.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.22), residues: 1355
  helix:  1.11 (0.20), residues: 643
  sheet: -0.47 (0.38), residues: 170
  loop : -1.16 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 274 
 TYR   0.022   0.002   TYR B  31 
 PHE   0.016   0.002   PHE B 654 
 TRP   0.030   0.003   TRP A 137 
 HIS   0.005   0.001   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (10976)
  covalent geometry    : angle       0.76798 (14869)
  hydrogen bonds       : bond        0.03778 (  552)
  hydrogen bonds       : angle       5.24763 ( 1557)

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

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

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2710 Ramachandran restraints generated.
    1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8343 (mpt180) cc_final: 0.7984 (mpp-170)
REVERT: A  143 PHE cc_start: 0.6448 (m-80) cc_final: 0.6145 (m-10)
REVERT: A  222 LEU cc_start: 0.8489 (mt) cc_final: 0.8122 (pt)
REVERT: A  229 ASN cc_start: 0.9069 (t0) cc_final: 0.8773 (t0)
REVERT: A  382 LEU cc_start: 0.8049 (mt) cc_final: 0.7701 (tp)
REVERT: A  432 GLU cc_start: 0.8577 (tt0) cc_final: 0.7847 (tp30)
REVERT: A  441 ASP cc_start: 0.8924 (m-30) cc_final: 0.8492 (p0)
REVERT: A  552 LEU cc_start: 0.8949 (mm) cc_final: 0.8696 (mp)
REVERT: A  615 PRO cc_start: 0.7441 (Cg_endo) cc_final: 0.6362 (Cg_exo)
REVERT: A  616 ASN cc_start: 0.6813 (t0) cc_final: 0.6316 (t0)
REVERT: A  784 GLU cc_start: 0.8846 (pm20) cc_final: 0.8597 (pm20)
REVERT: B   73 TYR cc_start: 0.6803 (p90) cc_final: 0.6343 (p90)
REVERT: B  386 ASP cc_start: 0.7231 (p0) cc_final: 0.6908 (p0)
REVERT: B  524 GLU cc_start: 0.8047 (pt0) cc_final: 0.6552 (mm-30)
REVERT: B  529 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8070 (tm-30)
REVERT: B  644 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8149 (tptp)
REVERT: B  692 MET cc_start: 0.5268 (ttt) cc_final: 0.3929 (ttt)
REVERT: B  717 ASN cc_start: 0.8041 (t0) cc_final: 0.7169 (t0)
REVERT: B  725 PHE cc_start: 0.6975 (m-80) cc_final: 0.5819 (m-10)
REVERT: B  739 MET cc_start: 0.6197 (ttt) cc_final: 0.5869 (ttt)
REVERT: B  752 HIS cc_start: 0.8393 (p-80) cc_final: 0.8139 (p-80)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1291
  time to fit residues: 33.6933
Evaluate side-chains
  157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 117 optimal weight:    0.2980
   chunk 15 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 128 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 125 optimal weight:    6.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 752 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.071830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.063267 restraints weight = 71576.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.064697 restraints weight = 51549.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.065793 restraints weight = 39035.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.066659 restraints weight = 30682.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.067311 restraints weight = 24722.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.7632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10976  Z= 0.143
  Angle     :  0.743   9.427  14869  Z= 0.372
  Chirality :  0.045   0.215   1706
  Planarity :  0.005   0.049   1934
  Dihedral  :  6.403 116.823   1532
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.22), residues: 1355
  helix:  1.29 (0.20), residues: 645
  sheet: -0.30 (0.39), residues: 162
  loop : -1.11 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 172 
 TYR   0.021   0.002   TYR B  31 
 PHE   0.013   0.001   PHE B 654 
 TRP   0.032   0.002   TRP A 137 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10976)
  covalent geometry    : angle       0.74333 (14869)
  hydrogen bonds       : bond        0.03607 (  552)
  hydrogen bonds       : angle       5.07125 ( 1557)

===============================================================================
Job complete
usr+sys time: 1622.01 seconds
wall clock time: 28 minutes 58.17 seconds (1738.17 seconds total)